6693323
Automated Surface Matching Using Mutual Information Applied to Riemann Surface Structures
Many medical imaging applications require the computation of dense correspondence vector fields that match one surface with another. To avoid the need for a large set of manually-defined landmarks to constrain these surface correspondences, we developed an algorithm to automate the matching of surface features. It extends the mutual information method to automatically match general 3D surfaces (including surfaces with a branching topology). First, we use holomorphic 1-forms to induce consistent conformal grids on both surfaces. High genus surfaces are mapped to a set of rectangles in the Euclidean plane, and closed genus-zero surfaces are mapped to the sphere. Mutual information is used as a cost functional to drive a fluid flow in the parameter domain that optimally aligns stable geometric features (mean curvature and the conformal factor) in the 2D parameter domains. A diffeomorphic surface-to-surface mapping is then recovered that matches anatomy in 3D. We also present a spectral method that ensures that the grids induced on the target surface remain conformal when pulled through the correspondence field. Using the chain rule, we express the gradient of the mutual information between surfaces in the conformal basis of the source surface. This finite-dimensional linear space generates all conformal reparameterizations of the surface. We apply the method to hippocampal surface registration, a key step in subcortical shape analysis in Alzheimer's disease and schizophrenia.
3357707
A method for document zone content classification
This paper describes an algorithm to classify each given document zone into one of nine classes and provides a protocol for its performance evaluation. The classification scheme uses an optimized binary decision tree and Viterbi algorithm for HMM to find the optimal solution. Our algorithm was trained and tested on a total of 24,177 zones within the 1600 images from UWCDROM III database. Its accuracy rate is 98.45% with a mean false alarm rate of 0.50%.
2521415
Brain Surface Conformal Parameterization
We develop a general approach that uses holomorphic 1forms 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. We can then automatically partition the surface using a critical graph that connects zero points in the conformal structure on the surface. The trajectories of iso-parametric curves canonically partition a surface into patches. Each of these patches is either a topological disk or a cylinder and can be conformally mapped to a parallelogram by integrating a holomorphic 1-form defined on the surface. The resulting surface subdivision and the parameterizations of the components are intrinsic and stable. To illustrate the technique, we computed conformal structures for several types of anatomical surfaces in MRI scans of the brain, including the cortex, hippocampus, and lateral ventricles. We found that the resulting parameterizations were consistent across subjects, even for branching structures such as the ventricles, which are otherwise difficult to parameterize. Compared with other variational approaches based on surface inflation, our technique works on surfaces with arbitrary complexity while guaranteeing minimal distortion in the parameterization. It also generates grids on surfaces for PDE-based signal processing.
3331857
Table Detection via Probability Optimization
In this paper, we define the table detection problem as a probability optimization problem. We begin, as we do in our previous algorithm, finding and validating each detected table candidates. We proceed to compute a set of probability measurements for each of the table entities. The computation of the probability measurements takes into consideration tables, table text separators and table neighboring text blocks. Then, an iterative updating method is used to optimize the page segmentation probability to obtain the final result. This new algorithm shows a great improvement over our previous algorithm. The training and testing data set for the algorithm include 1, 125 document pages having 518 table entities and a total of 10, 934 cell entities. Compared with our previous work, it raised the accuracy rate to 95.67% from 90.32% and to 97.05% from 92.04%.
5987381
Algorithm performance contest
This contest involved the running and evaluation of computer vision and pattern recognition techniques on different data sets with known groundwidth. The contest included three areas; binary shape recognition, symbol recognition and image flow estimation. A package was made available for each area. Each package contained either real images with manual groundtruth or programs to generate data sets of ideal as well as noisy images with known groundtruth. They also contained programs to evaluate the results of an algorithm according to the given groundtruth. These evaluation criteria included the generation of confusion matrices, computation of the misdetection and false alarm rates and other performance measures suitable for the problems. The paper summarizes the data generation for each area and experimental results for a total of six participating algorithms.
5121588
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. Each of these patches can be conformally mapped to a parallelogram. The resulting surface subdivision and the parameterizations of the components are intrinsic and stable. To illustrate the technique, we computed conformal structures for several types of anatomical surfaces in MRI scans of the brain, including the cortex, hippocampus, and lateral ventricles. We found that the resulting parameterizations were consistent across subjects, even for branching structures such as the ventricles, which are otherwise difficult to parameterize. Compared with other variational approaches based on surface inflation, our technique works on surfaces with arbitrary complexity while guaranteeing minimal distortion in the parameterization. It also offers a way to explicitly match landmark curves in anatomical surfaces such as the cortex, providing a surface-based framework to compare anatomy statistically and to generate grids on surfaces for PDE-based signal processing.
10936975
Quantifying Evolving Processes in Multimodal 3D Medical Images
Quantitative measurements of changes in evolving brain pathology, such as multiple sclerosis lesions and brain tumors, are important for clinicians to perform pertinent diagnoses and to help in patient follow-up. Lesions or tumors can vary over time in size, shape, location and composition because of natural pathological processes or the effect of a drug treatment or therapy. In the past, people have used as a quantitative measurement the change in total or regional lesion/tumor volume. In this paper we propose a new model to quantify changes in evolving processes in multimodal 3D medical images. We believe this model reflects changes in pathology more accurately because it simultaneously takes into account information in multiple imaging modalities and the location of lesion/tumor voxels. We demonstrate the effectiveness of this model with experiments on synthetic lesion data.
6932570
3D Surface Matching and Recognition Using Conformal Geometry
3D surface matching is a fundamental issue in computer vision with many applications such as shape registration, 3D object recognition and classification. However, surface matching with noise, occlusion and clutter is a challenging problem. In this paper, we analyze a family of conformal geometric maps including harmonic maps, conformal maps and least squares conformal maps with regards to 3D surface matching. As a result, we propose a novel and computationally efficient surface matching framework that uses least squares conformal maps. According to conformal geometry theory, each 3D surface with disk topology can be mapped to a 2D domain through a global optimization and the resulting map is a diffeomorphism, i.e., one-to-one and onto. This allows us to simplify the 3D surface-matching problem to a 2D image-matching problem, by comparing the resulting 2D conformal geometric maps, which are stable, insensitive to resolution changes and robust to occlusion and noise. Therefore, highly accurate and efficient 3D surface matching algorithms can be achieved by using conformal geometric maps. Finally, the performance of conformal geometric maps is evaluated and analyzed comprehensively in 3D surface matching with occlusion, noise and resolution variation. We also provide a series of experiments on real 3D face data that achieve high recognition rates.
6558099
A Generative Method for Textured Motion: Analysis and Synthesis
Natural scenes contain rich stochastic motion patterns which are characterized by the movement of a large number of small elements, such as falling snow, raining, flying birds, firework and waterfall. In this paper, we call these motion patterns textured motion and present a generative method that combines statistical models and algorithms from both texture and motion analysis. The generative method includes the following three aspects. 1). Photometrically, an image is represented as a superposition of linear bases in atomic decomposition using an overcomplete dictionary, such as Gabor or Laplacian. Such base representation is known to be generic for natural images, and it is low dimensional as the number of bases is often 100 times smaller than the number of pixels. 2). Geometrically, each moving element (called moveton), such as the individual snowflake and bird, is represented by a deformable template which is a group of several spatially adjacent bases. Such templates are learned through clustering. 3). Dynamically, the movetons are tracked through the image sequence by a stochastic algorithm maximizing a posterior probability. A classic second order Markov chain model is adopted for the motion dynamics. The sources and sinks of the movetons are modeled by birth and death maps. We adopt an EM-like stochastic gradient algorithm for inference of the hidden variables: bases, movetons, birth/death maps, parameters of the dynamics. The learned models are also verified through synthesizing random textured motion sequences which bear similar visual appearance with the observed sequences.
793367
3D Brain surface matching based on geodesics and local geometry
The non-rigid registration of surfaces is a complex and difficult task for which there are many important applications, such as comparing shape between deformable objects and comparing associated function. This paper presents a new approach for brain surface matching by determining the correspondence of 3D point sets between pairs of surfaces. The algorithm is based on shape using a combination of geodesic distance and surface curvature. There are two major procedures involved. An initial sparse set of corresponding points is first generated by matching local geometrical features. Geodesic distance interpolation is then employed hierarchically in order to capture the complex surface. By this scheme, surface correspondence and triangulation are computed simultaneously. Experiments applied to human cerebral cortical surfaces are shown to evaluate the approach. It is shown that the proposed method performs well for both surface matching and surface shape recovery.
27423282
Visualization of DNA/RNA Structure using Temporal CGRs
We present a new DNA/RNA sequence visualization technique, Temporal Chaos Game Representation (TCGR), which is an extension of Frequency Chaos Game Representation (FCGR). Unlike earlier CGR variants, TCGR illustrates the distribution of nucleotide sub-patterns at different positions within a sequence, and it can be applied to sets of sequences as well as individual sequences. TCGRs are suitable for short or long sequences. Preliminary experiments examining patterns of nucleotide occurrences in micro-RNA data illustrate not only the informative nature of the images, but clearly indicate the variability of distributions based on position, and the similarity and differences of distributions across various species