3D Segmentation of Rodent Brain Structures Using Hierarchical Shape Priors and Deformable Models (original) (raw)
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3D segmentation of rodent brain structures using Active Volume Model with shape priors
2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2011
In this paper, we propose a method to segment multiple rodent brain structures simultaneously. This method combines deformable models and hierarchical shape priors within one framework. The deformation module employs both gradient and appearance information to generate image forces to deform the shape. The shape prior module uses Principal Component Analysis to hierarchically model the multiple structures at both global and local levels. At the global level, the statistics of relative positions among different structures are modeled. At the local level, the shape statistics within each structure is learned from training samples. Our segmentation method adaptively employs both priors to constrain the intermediate deformation result. This prior constraint improves the robustness of the model and benefits the segmentation accuracy. Another merit of our prior module is that the size of the training data can be small, because the shape prior module models each structure individually and combines them using global statistics. This scheme can preserve shape details better than directly applying PCA on all structures. We use this method to segment rodent brain structures, such as the cerebellum, the left and right striatum, and the left and right hippocampus. The experiments show that our method works effectively and this hierarchical prior improves the segmentation performance.
3D segmentation of rodent brains using deformable models and variational methods
2009 IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2009
3D functional segmentation of brain images is important in understating the relationships between anatomy and mental diseases in brains. Volumetric analysis of various brain structures such as the cerebellum plays a critical role in studying the structural changes in brain regions as a function of development, trauma, or neurodegeneratioin. Although various segmentation methods in clinical studies have been proposed, many of them require a priori knowledge about the locations of the structures of interest, which prevents the fully automatic segmentation. Besides, the topological changes of structures are difficult to detect. In this paper, we present a novel method for detecting and locating the brain structures of interest that can be used for the fully automatic 3D functional segmentation of rodent brain MR images. The presented method is based on active shape model (ASM), Metamorph models and variational techniques. It focuses on detecting the topological changes of brain structures based on a novel volume ratio criteria. The mean successful rate of the topological change detection shows 86.6% accuracy compared to the expert identified ground truth.
A Coarse-to-fine Shape Prior for Probabilistic Segmentations Using A Deformable M-rep
Training a shape prior has been potent scheme for anatomical object segmentations, especially for images with noisy or weak intensity patterns. When the shape representation lives in a high dimensional space, Principal Component Analysis (PCA) is often used to calculate a low dimensional variation subspace from frequently limited number of training samples. However, the eigenmodes of the subspace tend to keep the coarse variation of the shape only, losing the detailed localized variability which is crucial to accurate segmentations. In this paper, we propose a coarse-to-fine shape prior for probabilistic segmentation to enable local refinement, using a deformable medial representation, called the m-rep.
Multi-object deformable templates dedicated to the segmentation of brain deep structures
Lecture Notes in Computer Science, 1998
We propose a new way of embedding shape distributions in a topological deformable template. These distributions rely on global shape descriptors corresponding to the 3D moment invariants. In opposition to usual Fourier-like descriptors, they can be updated during deformations at a relatively low cost. The moment-based distributions are included in a framework allowing the management of several simultaneously deforming objects. This framework is dedicated to the segmentation of brain deep nuclei in 3D MR images. The paper focuses on the learning of the shape distributions, on the initialization of the topological model and on the multi-resolution energy minimization process. Results are presented showing the segmentation of twelve brain deep structures.
2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2009
We present a new active contour-based, statistical method for simultaneous volumetric segmentation of multiple subcortical structures in the brain. Neighboring anatomical structures in the human brain exhibit co-dependencies which can aid in segmentation, if properly analyzed and modeled. Motivated by this observation, we formulate the segmentation problem as a maximum a posteriori estimation problem, in which we incorporate statistical prior models on the shapes and inter-shape (relative) poses of the structures of interest. This provides a principled mechanism to bring high level information about the shapes and the relationships of anatomical structures into the segmentation problem. For learning the prior densities based on training data, we use a nonparametric multivariate kernel density estimation framework. We combine these priors with data in a variational framework, and develop an active contour-based iterative segmentation algorithm. We test our method on the problem of volumetric segmentation of basal ganglia structures in magnetic resonance (MR) images and present a quantitative performance analysis. We compare our technique with existing methods and demonstrate the improvements it provides in terms of segmentation accuracy.
Knowledge-based deformable surface model with application to segmentation of brain structures in MRI
Medical Imaging 2001: Image Processing, 2001
We have developed a knowledge-based deformable surface for segmentation of medical images. This work has been done in the context of segmentation of hippocampus from brain MRI, due to its challenge and clinical importance. The model has a polyhedral discrete structure and is initialized automatically by analyzing brain MRI sliced by slice, and finding few landmark features at each slice using an expert system. The expert system decides on the presence of the hippocampus and its general location in each slice. The landmarks found are connected together by a triangulation method, to generate a closed initial surface. The surface deforms under defined internal and external force terms thereafter, to generate an accurate and reproducible boundary for the hippocampus. The anterior and posterior (AP) limits of the hippocampus is estimated by automatic analysis of the location of brain stem, and some of the features extracted in the initialization process. These data are combined together with a priori knowledge using Bayes method to estimate a probability density function (pdf) for the length of the structure in sagittal direction. The hippocampus AP limits are found by optimizing this pdf. The model is tested on real clinical data and the results show very good model performance 1 .
IEEE Transactions on Medical Imaging, 2000
T HIS paper presents a new active contour-based, statistical method for simultaneous volumetric segmentation of multiple subcortical structures in the brain. In biological tissues, such as the human brain, neighboring structures exhibit codependencies which can aid in segmentation, if properly analyzed and modeled. Motivated by this observation, we formulate the segmentation problem as a maximum a posteriori estimation problem, in which we incorporate statistical prior models on the shapes and inter-shape (relative) poses of the structures of interest. This provides a principled mechanism to bring high level information about the shapes and the relationships of anatomical structures into the segmentation problem. For learning the prior densities we use a nonparametric multivariate kernel density estimation framework. We combine these priors with data in a variational framework and develop an active contour-based iterative segmentation algorithm. We test our method on the problem of volumetric segmentation of basal ganglia structures in magnetic resonance (MR) images. We present a set of 2D and 3D experiments as well as a quantitative performance analysis. In addition, we perform a comparison to several existent segmentation methods and demonstrate the improvements provided by our approach in terms of segmentation accuracy.
Coupled nonparametric shape priors for segmentation of multiple basal ganglia structures
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2008
This paper presents a new method for multiple structure segmentation, using a maximum a posteriori (MAP) estimation framework, based on prior shape densities involving nonparametric multivariate kernel density estimation of multiple shapes. Our method is motivated by the observation that neighboring or coupling structures in medical images generate configurations and co-dependencies which could potentially aid in segmentation if properly exploited. Our technique allows simultaneous segmentation of multiple objects, where highly contrasted, easy-to-segment structures can help improve the segmentation of weakly contrasted objects. We demonstrate the effectiveness of our method on both synthetic images and real magnetic resonance images (MRI) for segmentation of basal ganglia structures.
Multi-scale 3-D Deformable Model Segmentation Based on Medial Description
Lecture Notes in Computer Science, 2001
This paper presents a Bayesian multi-scale three dimensional deformable template approach based on a medial representation for the segmentation and shape characterization of anatomical objects in medical imagery. Prior information about the geometry and shape of the anatomical objects under study is incorporated via the construction of exemplary templates. The anatomical variability is accommodated in the Bayesian framework by defining probabilistic transformations on these templates. The modeling approach taken in this paper for building exemplary templates and associated transformations is based on a multi-scale medial representation. The transformations defined in this framework are parameterized directly in terms of natural shape operations, such as thickening and bending, and their location. Quantitative validation results are presented on the automatic segmentation procedure developed for the extraction of the kidney parenchyma-including the renal pelvis-in subjects undergoing radiation treatment for cancer. We show that the segmentation procedure developed in this paper is efficient and accurate to within the voxel resolution of the imaging modality.
A Hybrid Geometric–Statistical Deformable Model for Automated 3-D Segmentation in Brain MRI
IEEE Transactions on Biomedical Engineering, 2000
We present a novel 3-D deformable model-based approach for accurate, robust, and automated tissue segmentation of brain MRI data of single as well as multiple magnetic resonance sequences. The main contribution of this study is that we employ an edge-based geodesic active contour for the segmentation task by integrating both image edge geometry and voxel statistical homogeneity into a novel hybrid geometric-statistical feature to regularize contour convergence and extract complex anatomical structures. We validate the accuracy of the segmentation results on simulated brain MRI scans of both single T1-weighted and multiple T1/T2/PD-weighted sequences. We also demonstrate the robustness of the proposed method when applied to clinical brain MRI scans. When compared to a current state-of-the-art regionbased level-set segmentation formulation, our white matter and gray matter segmentation resulted in significantly higher accuracy levels with a mean improvement in Dice similarity indexes of 8.55% (p < 0.0001) and 10.18% (p < 0.0001), respectively. Index Terms-3-D image segmentation, brain segmentation, deformable models, geodesic active contour.