Automated Segmentation of Mouse Brain Images Using Multi-Atlas Multi-ROI Deformation and Label Fusion

We propose an automated multi-atlas and multi-ROI based segmentation method for both skull-stripping of mouse brain and the ROI-labeling of mouse brain structures from the three dimensional (3D) magnetic resonance images (MRI). Three main steps are involved in our method. First, a region of interest (ROI) guided warping algorithm is designed to register multi-atlas images to the subject space, by considering more on the matching of image contents around the ROI boundaries which are more important for ROI labeling. Then, a multi-atlas and multi-ROI based deformable segmentation method is adopted to refine the ROI labeling result by deforming each ROI surface via boundary recognizers (i.e., SVM classifiers) trained on local surface patches. Finally, a local-mutual-information (MI) based multi-label fusion technique is proposed for allowing the atlases with better local image similarity with the subject to have more contributions in label fusion. The experimental results show that our method works better than the conventional methods on both in vitro and in vivo mouse brain datasets

Development of cortical anatomical properties from early childhood to early adulthood

Human brain matures in temporal and regional heterogeneity, with some areas matured at early adulthood. In this study, the relationship of cortical structural developments between different cortical sheet regions is systematically analyzed using interregional correlation coefficient and network methods. Specifically, 951 longitudinal T1 brain MR images from 445 healthy subjects with ages from 3 to 20 years old are used. The result shows that the development of cortex reaches a turning point at around 7 years of age: a) the cortical thickness reaches its highest value and also the cortical folding becomes stable at this age; b) both global and local efficiencies of anatomical correlation networks reach the lowest and highest values at this age, respectively; and c) the change of anatomical correlation networks reach the highest level at this age, and the convergence of different anatomical correlation networks starts to decrease from this age. These results might inspire more studies on why there exists a turning point at this age from different viewpoints. For example, is there any change of synaptic pruning, or is it related to the starting of school life? And how can we benefit from this in the real life

Consistent reconstruction of cortical surfaces from longitudinal brain MR images

Accurate and consistent reconstruction of cortical surfaces from longitudinal human brain MR images is of great importance in studying longitudinal subtle change of the cerebral cortex. This paper presents a novel deformable surface method for consistent and accurate reconstruction of inner, central and outer cortical surfaces from longitudinal brain MR images. Specifically, the cortical surfaces of the group-mean image of all aligned longitudinal images of the same subject are first reconstructed by a deformable surface method, which is driven by a force derived from the Laplace’s equation. And then the longitudinal cortical surfaces are consistently reconstructed by jointly deforming the cortical surfaces of the group-mean image to all longitudinal images. The proposed method has been successfully applied to two sets of longitudinal human brain MR images. Both qualitative and quantitative experimental results demonstrate the accuracy and consistency of the proposed method. Furthermore, the reconstructed longitudinal cortical surfaces are used to measure the longitudinal changes of cortical thickness in both normal and diseased groups, where the overall decline trend of cortical thickness has been clearly observed. Meanwhile, the longitudinal cortical thickness also shows its potential in distinguishing different clinical groups

3D cell nuclei segmentation based on gradient flow tracking

<p>Abstract</p> <p>Background</p> <p>Reliable segmentation of cell nuclei from three dimensional (3D) microscopic images is an important task in many biological studies. We present a novel, fully automated method for the segmentation of cell nuclei from 3D microscopic images. It was designed specifically to segment nuclei in images where the nuclei are closely juxtaposed or touching each other. The segmentation approach has three stages: 1) a gradient diffusion procedure, 2) gradient flow tracking and grouping, and 3) local adaptive thresholding.</p> <p>Results</p> <p>Both qualitative and quantitative results on synthesized and original 3D images are provided to demonstrate the performance and generality of the proposed method. Both the over-segmentation and under-segmentation percentages of the proposed method are around 5%. The volume overlap, compared to expert manual segmentation, is consistently over 90%.</p> <p>Conclusion</p> <p>The proposed algorithm is able to segment closely juxtaposed or touching cell nuclei obtained from 3D microscopy imaging with reasonable accuracy.</p

Meta-Network Analysis of Structural Correlation Networks Provides Insights Into Brain Network Development

Analysis of developmental brain networks is fundamentally important for basic developmental neuroscience. In this paper, we focus on the temporally-covarying connection patterns, called meta-networks, and develop a new mathematical model for meta-network decomposition. With the proposed model, we decompose the developmental structural correlation networks of cortical thickness into five meta-networks. Each meta-network exhibits a distinctive spatial connection pattern, and its covarying trajectory highlights the temporal contribution of the meta-network along development. Systematic analysis of the meta-networks and covarying trajectories provides insights into three important aspects of brain network development

Mapping Region-Specific Longitudinal Cortical Surface Expansion from Birth to 2 Years of Age

The human cerebral cortex develops rapidly and dynamically in the first 2 years of life. It has been shown that cortical surface expansion from term infant to adult is highly nonuniform in a cross-sectional study. However, little is known about the longitudinal cortical surface expansion during early postnatal stages. In this article, we generate the first longitudinal surface-based atlases of human cortical structures at 0, 1, and 2 years of age from 73 healthy subjects. On the basis of the surface-based atlases, we study the longitudinal cortical surface expansion in the first 2 years of life and find that cortical surface expansion is age related and region specific. In the first year, cortical surface expands dramatically, with an average expansion of 1.80 times. In particular, regions of superior and medial temporal, superior parietal, medial orbitofrontal, lateral anterior prefrontal, occipital cortices, and postcentral gyrus expand relatively larger than other regions. In the second year, cortical surface still expands substantially, with an average expansion of 1.20 times. In particular, regions of superior and middle frontal, orbitofrontal, inferior temporal, inferior parietal, and superior parietal cortices expand relatively larger than other regions. These region-specific patterns of cortical surface expansion are related to cognitive and functional development at these stages

Measuring the dynamic longitudinal cortex development in infants by reconstruction of temporally consistent cortical surfaces

Quantitative measurement of the dynamic longitudinal cortex development during early postnatal stages is of great importance to understand the early cortical structural and functional development. Conventional methods usually reconstruct the cortical surfaces of longitudinal images from the same subject independently, which often generate longitudinally-inconsistent cortical surfaces and thus lead to inaccurate measurement of cortical changes, especially for vertex-wise mapping of cortical development. This paper aims to address this problem by presenting a method to reconstruct temporally-consistent cortical surfaces from longitudinal infant brain MR images, for accurate and consistent measurement of the dynamic cortex development in infants. Specifically, the longitudinal development of the inner cortical surface is first modeled by a deformable growth sheet with elasto-plasticity property to establish longitudinally smooth correspondences of the inner cortical surfaces. Then, the modeled longitudinal inner cortical surfaces are jointly deformed to locate both inner and outer cortical surfaces with a spatial-temporal deformable surface method. The method has been applied to 13 healthy infants, each with 6 serial MR scans acquired at 2 weeks, 3 months, 6 months, 9 months, 12 months and 18 months of age. Experimental results showed that our method with the incorporated longitudinal constraints can reconstruct the longitudinally-dynamic cortical surfaces from serial infant MR images more consistently and accurately than the previously published methods. By using our method, for the first time, we can characterize the vertex-wise longitudinal cortical thickness development trajectory at multiple time points in the first 18 months of life. Specifically, we found the highly age-related and regionally-heterogeneous developmental trajectories of the cortical thickness during this period, with the cortical thickness increased most from 3 to 6 months (16.2%) and least from 9 to 12 months (less than 0.1%). Specifically, the central sulcus only underwent significant increase of cortical thickness from 6 to 9 months and the occipital cortex underwent significant increase from 0 to 9 months, while the frontal, temporal and parietal cortices grew continuously in this first 18 months of life. The adult-like spatial patterns of cortical thickness were generally present at 18 months of age. These results provided detailed insights into the dynamic trajectory of the cortical thickness development in infants

Longitudinal development of cortical thickness, folding, and fiber density networks in the first 2 years of life: Longitudinal Development of Cortical Thickness, Folding, and Fiber Density Networks

Quantitatively characterizing the development of cortical anatomical networks during the early stage of life plays an important role in revealing the relationship between cortical structural connection and high-level functional development. The development of correlation networks of cortical-thickness, cortical folding, and fiber-density is systematically analyzed in this article to study the relationship between different anatomical properties during the first 2 years of life. Specifically, longitudinal MR images of 73 healthy subjects from birth to 2 year old are used. For each subject at each time point, its measures of cortical thickness, cortical folding, and fiber density are projected to its cortical surface that has been partitioned into 78 cortical regions. Then, the correlation matrices for cortical thickness, cortical folding, and fiber density at each time point can be constructed, respectively, by computing the inter-regional Pearson correlation coefficient (of any pair of ROIs) across all 73 subjects. Finally, the presence/ absence pattern (i.e., binary pattern) of the connection network is constructed from each inter-regional correlation matrix, and its statistical and anatomical properties are adopted to analyze the longitudinal development of anatomical networks. The results show that the development of anatomical network could be characterized differently by using different anatomical properties (i.e., using cortical thickness, cortical folding, or fiber density)

Spatiotemporal Analysis of Developing Brain Networks

Recent advances in MRI have made it easier to collect data for studying human structural and functional connectivity networks. Computational methods can reveal complex spatiotemporal dynamics of the human developing brain. In this paper, we propose a Developmental Meta-network Decomposition (DMD) method to decompose a series of developmental networks into a set of Developmental Meta-networks (DMs), which reveal the underlying changes in connectivity over development. DMD circumvents the limitations of traditional static network decomposition methods by providing a novel exploratory approach to capture the spatiotemporal dynamics of developmental networks. We apply this method to structural correlation networks of cortical thickness across subjects at 3–20 years of age, and identify four DMs that smoothly evolve over three stages, i.e., 3–6, 7–12, and 13–20 years of age. We analyze and highlight the characteristic connections of each DM in relation to brain development

Knowledge-Guided Robust MRI Brain Extraction for Diverse Large-Scale Neuroimaging Studies on Humans and Non-Human Primates

Accurate and robust brain extraction is a critical step in most neuroimaging analysis pipelines. In particular, for the large-scale multi-site neuroimaging studies involving a significant number of subjects with diverse age and diagnostic groups, accurate and robust extraction of the brain automatically and consistently is highly desirable. In this paper, we introduce population-specific probability maps to guide the brain extraction of diverse subject groups, including both healthy and diseased adult human populations, both developing and aging human populations, as well as non-human primates. Specifically, the proposed method combines an atlas-based approach, for coarse skull-stripping, with a deformable-surface-based approach that is guided by local intensity information and population-specific prior information learned from a set of real brain images for more localized refinement. Comprehensive quantitative evaluations were performed on the diverse large-scale populations of ADNI dataset with over 800 subjects (55∼90 years of age, multi-site, various diagnosis groups), OASIS dataset with over 400 subjects (18∼96 years of age, wide age range, various diagnosis groups), and NIH pediatrics dataset with 150 subjects (5∼18 years of age, multi-site, wide age range as a complementary age group to the adult dataset). The results demonstrate that our method consistently yields the best overall results across almost the entire human life span, with only a single set of parameters. To demonstrate its capability to work on non-human primates, the proposed method is further evaluated using a rhesus macaque dataset with 20 subjects. Quantitative comparisons with popularly used state-of-the-art methods, including BET, Two-pass BET, BET-B, BSE, HWA, ROBEX and AFNI, demonstrate that the proposed method performs favorably with superior performance on all testing datasets, indicating its robustness and effectiveness