Normal Estimation of a Transparent Object Using a Video.

Reconstructing transparent objects is a challenging problem. While producing reasonable results for quite complex objects, existing approaches require custom calibration or somewhat expensive labor to achieve high precision. When an overall shape preserving salient and fine details is sufficient, we show in this paper a significant step toward solving the problem when the object's silhouette is available and simple user interaction is allowed, by using a video of a transparent object shot under varying illumination.

Brain surface conformal parameterization with the Ricci flow.

In brain mapping research, parameterized 3-D surface models are of great interest for statistical comparisons of anatomy, surface-based registration, and signal processing. Here, we introduce the theories of continuous and discrete surface Ricci flow, which can create Riemannian metrics on surfaces with arbitrary topologies with user-defined Gaussian curvatures. The resulting conformal parameterizations have no singularities and they are intrinsic and stable.

Independent component analysis-based classification of Alzheimer's disease MRI data.

There is an unmet medical need to identify neuroimaging biomarkers that allow us to accurately diagnose and monitor Alzheimer's disease (AD) at its very early stages and to assess the response to AD-modifying therapies. To a certain extent, volumetric and functional magnetic resonance imaging (fMRI) studies can detect changes in structure, cerebral blood flow, and blood oxygenation that distinguish AD and mild cognitive impairment (MCI) subjects from healthy control (HC) subjects. However, it has been challenging to use fully automated MRI analytic methods to identify potential AD neuroimaging biomarkers.

Nonlocal Mumford-Shah regularizers for color image restoration.

We propose here a class of restoration algorithms for color images, based upon the Mumford-Shah (MS) model and nonlocal image information. The Ambrosio-Tortorelli and Shah elliptic approximations are defined to work in a small local neighborhood, which are sufficient to denoise smooth regions with sharp boundaries. However, texture is nonlocal in nature and requires semilocal/non-local information for efficient image denoising and restoration.

Multivariate tensor-based morphometry on surfaces: application to mapping ventricular abnormalities in HIV/AIDS.

Here we developed a new method, called multivariate tensor-based surface morphometry (TBM), and applied it to study lateral ventricular surface differences associated with HIV/AIDS. Using concepts from differential geometry and the theory of differential forms, we created mathematical structures known as holomorphic one-forms, to obtain an efficient and accurate conformal parameterization of the lateral ventricular surfaces in the brain. The new meshing approach also provides a natural way to register anatomical surfaces across subjects, and improves on prior methods as it handles surfaces that branch and join at complex 3D junctions.

Unsupervised multiphase segmentation: a phase balancing model.

Variational models have been studied for image segmentation application since the Mumford-Shah functional was introduced in the late 1980s. In this paper, we focus on multiphase segmentation with a new regularization term that yields an unsupervised segmentation model. We propose a functional that automatically chooses a favorable number of phases as it segments the image.

LAPLACE-BELTRAMI NODAL COUNTS: A NEW SIGNATURE FOR 3D SHAPE ANALYSIS.

In this paper we develop a new approach of analyzing 3D shapes based on the eigen-system of the Laplace-Beltrami operator. While the eigenvalues of the Laplace-Beltrami operator have been used previously in shape analysis, they are unable to differentiate isospectral shapes. To overcome this limitation, we propose here a new signature based on nodal counts of the eigenfunctions.

Source reconstruction for spectrally-resolved bioluminescence tomography with sparse a priori information.

Through restoration of the light source information in small animals in vivo, optical molecular imaging, such as fluorescence molecular tomography (FMT) and bioluminescence tomography (BLT), can depict biological and physiological changes observed using molecular probes. A priori information plays an indispensable role in tomographic reconstruction. As a type of a priori information, the sparsity characteristic of the light source has not been sufficiently considered to date.

Teichmöller shape space theory and its application to brain morphometry.

Here we propose a novel method to compute Teichmiiller shape space based shape index to study brain morphometry. Such a shape index is intrinsic, and invariant under conformal transformations, rigid motions and scaling. We conformally map a genus-zero open boundary surface to the Poincaré disk with the Yamabe flow method.

Multivariate tensor-based brain anatomical surface morphometry via holomorphic one-forms.

Here we introduce multivariate tensor-based surface morphometry using holomorphic one-forms to study brain anatomy. We computed new statistics from the Riemannian metric tensors that retain the full information in the deformation tensor fields. We introduce two different holomorphic one-forms that induce different surface conformal parameterizations.

Conformal slit mapping and its applications to brain surface parameterization.

We propose a method that computes a conformal mapping from a multiply connected mesh to the so-called slit domain, which consists of a canonical rectangle or disk in which 3D curved landmarks on the original surfaces are mapped to concentric or parallel lines in the slit domain. In this paper, we studied its application to brain surface parameterization. After cutting along some landmark curve features on surface models of the cerebral cortex, we obtain multiple connected domains.

Level set method for positron emission tomography.

In positron emission tomography (PET), a radioactive compound is injected into the body to promote a tissue-dependent emission rate. Expectation maximization (EM) reconstruction algorithms are iterative techniques which estimate the concentration coefficients that provide the best fitted solution, for example, a maximum likelihood estimate. In this paper, we combine the EM algorithm with a level set approach.

Total variation regularization of matrix-valued images.

We generalize the total variation restoration model, introduced by Rudin, Osher, and Fatemi in 1992, to matrix-valued data, in particular, to diffusion tensor images (DTIs). Our model is a natural extension of the color total variation model proposed by Blomgren and Chan in 1998. We treat the diffusion matrix D implicitly as the product D = LL(T), and work with the elements of L as variables, instead of working directly on the elements of D.

Brain surface conformal parameterization using Riemann surface structure.

In medical imaging, parameterized 3-D surface models are useful for anatomical modeling and visualization, statistical comparisons of anatomy, and surface-based registration and signal processing. Here we introduce a parameterization method based on Riemann surface structure, which uses a special curvilinear net structure (conformal net) to partition the surface into a set of patches that can each be conformally mapped to a parallelogram. The resulting surface subdivision and the parameterizations of the components are intrinsic and stable (their solutions tend to be smooth functions and the boundary conditions of the Dirichlet problem can be enforced).

Strategies for identifying statistically significant dense regions in microarray data.

We propose and study the notion of dense regions for the analysis of categorized gene expression data and present some searching algorithms for discovering them. The algorithms can be applied to any categorical data matrices derived from gene expression level matrices. We demonstrate that dense regions are simple but useful and statistically significant patterns that can be used to 1) identify genes and/or samples of interest and 2) eliminate genes and/or samples corresponding to outliers, noise, or abnormalities.

Brain surface conformal parameterization with algebraic functions.

In medical imaging, parameterized 3D surface models are of great interest for anatomical modeling and visualization, statistical comparisons of anatomy, and surface-based registration and signal processing. Here we introduce a parameterization method based on algebraic functions. By solving the Yamabe equation with the Ricci flow method, we can conformally map a brain surface to a multi-hole disk.

A landmark-based brain conformal parametrization with automatic landmark tracking technique.

In this paper, we present algorithms to automatically detect and match landmark curves on cortical surfaces to get an optimized brain conformal parametrization. First, we propose an automatic landmark curve tracing method based on the principal directions of the local Weingarten matrix. Our algorithm obtains a hypothesized landmark curves using the Chan-Vese segmentation method, which solves a Partial Differential Equation (PDE) on a manifold with global conformal parameterization.

Dynamic cluster formation using level set methods.

Density-based clustering has the advantages for 1) allowing arbitrary shape of cluster and 2) not requiring the number of clusters as input. However, when clusters touch each other, both the cluster centers and cluster boundaries (as the peaks and valleys of the density distribution) become fuzzy and difficult to determine. We introduce the notion of cluster intensity function (CIF) which captures the important characteristics of clusters.

Optimization of brain conformal mapping with landmarks.

To compare and integrate brain data, data from multiple subjects are typically mapped into a canonical space. One method to do this is to conformally map cortical surfaces to the sphere. It is well known that any genus zero Riemann surface can be conformally mapped to a sphere.

Brain surface parameterization using Riemann surface structure.

We develop a general approach that uses holomorphic 1-forms to parameterize anatomical surfaces with complex (possibly branching) topology. Rather than evolve the surface geometry to a plane or sphere, we instead use the fact that all orientable surfaces are Riemann surfaces and admit conformal structures, which induce special curvilinear coordinate systems on the surfaces. Based on Riemann surface structure, we can then canonically partition the surface into patches.

Genus zero surface conformal mapping and its application to brain surface mapping.

It is well known that any genus zero surface can be mapped conformally onto the sphere and any local portion thereof onto a disk. However, it is not trivial to find a general method which finds a conformal mapping between two general genus zero surfaces. We propose a new variational method which can find a unique mapping between any two genus zero manifolds by minimizing the harmonic energy of the map.

Genus zero surface conformal mapping and its application to brain surface mapping.

We developed a general method for global conformal parameterizations based on the structure of the cohomology group of holomorphic one-forms for surfaces with or without boundaries (Gu and Yau, 2002), (Gu and Yau, 2003). For genus zero surfaces, our algorithm can find a unique mapping between any two genus zero manifolds by minimizing the harmonic energy of the map. In this paper, we apply the algorithm to the cortical surface matching problem.