Cell Image Segmentation with Kernel-Based Dynamic Clustering and an Ellipsoidal Cell Shape Model

AbstractIn this paper, we propose a novel approach to cell image segmentation under severe noise conditions by combining kernel-based dynamic clustering and a genetic algorithm. Our method incorporates a priori knowledge about cell shape. That is, an elliptical cell contour model is introduced to describe the boundary of the cell. Our method consists of the following components: (1) obtain the gradient image; (2) use the gradient image to obtain points which possibly belong to cell boundaries; (3) adjust the parameters of the elliptical cell boundary model to match the cell contour using a genetic algorithm. The method is tested on images of noisy human thyroid and small intestine cells

Model-Free, Regularized, Fast, and Robust Analytical Orientation Distribution Function Estimation

International audienceHigh Angular Resolution Imaging (HARDI) can better explore the complex micro-structure of white matter compared to Diffusion Tensor Imaging (DTI). Orientation Distribution Function (ODF) in HARDI is used to describe the probability of the fiber direction. There are two type definitions of the ODF, which were respectively proposed in Q-Ball Imaging (QBI) and Diffusion Spectrum Imaging (DSI). Some analytical reconstructions methods have been proposed to estimate these two type of ODFs from single shell HARDI data. However they all have some assumptions and intrinsic modeling errors. In this article, we propose, almost without any assumption, a uniform analytical method to estimate these two ODFs from DWI signals in q space, which is based on Spherical Polar Fourier Expression (SPFE) of signals. The solution is analytical and is a linear transformation from the q-space signal to the ODF represented by Spherical Harmonics (SH). It can naturally combines the DWI signals in dierent Q-shells. Moreover It can avoid the intrinsic Funk-Radon Transform (FRT) blurring error in QBI and it does not need any assumption of the signals, such as the multiple tensor model and mono/multi-exponential decay. We validate our method using synthetic data, phantom data and real data. Our method works well in all experiments, especially for the data with low SNR, low anisotropy and non-exponential decay

Fast, Model-Free , Analytical ODF Reconstruction from the Q-Space Signal

International audienceThe orientation distribution function (ODF) is very important in diffusion MRI. There are two types of ODFs. One is proposed using radial projection in Q-ball imaging [7]. Another one is the marginal pdf proposed in diffusion spectrum imaging (DSI) [8]. Since the marginal pdf is much sharper and mathematically correct, it could be more useful. Recently some reconstruction methods were proposed for this kind of ODF [1, 6]. They are both based on mono-exponential model, globally or locally, which has some intrinsic modeling error [4]. Although the authors in [1] extended the mono-exponential model to multi-exponential model, this multi-exponential model needs to be estimated non-linearly for every voxel and only in some special sampling scheme it has a analytical solution. Here we give a model-free analytical reconstruction method based on the Spherical Polar Fourier expression of the signal. It can estimate the ODF fast and analytically from the signal

Esub8: A novel tool to predict protein subcellular localizations in eukaryotic organisms

BACKGROUND: Subcellular localization of a new protein sequence is very important and fruitful for understanding its function. As the number of new genomes has dramatically increased over recent years, a reliable and efficient system to predict protein subcellular location is urgently needed. RESULTS: Esub8 was developed to predict protein subcellular localizations for eukaryotic proteins based on amino acid composition. In this research, the proteins are classified into the following eight groups: chloroplast, cytoplasm, extracellular, Golgi apparatus, lysosome, mitochondria, nucleus and peroxisome. We know subcellular localization is a typical classification problem; consequently, a one-against-one (1-v-1) multi-class support vector machine was introduced to construct the classifier. Unlike previous methods, ours considers the order information of protein sequences by a different method. Our method is tested in three subcellular localization predictions for prokaryotic proteins and four subcellular localization predictions for eukaryotic proteins on Reinhardt's dataset. The results are then compared to several other methods. The total prediction accuracies of two tests are both 100% by a self-consistency test, and are 92.9% and 84.14% by the jackknife test, respectively. Esub8 also provides excellent results: the total prediction accuracies are 100% by a self-consistency test and 87% by the jackknife test. CONCLUSIONS: Our method represents a different approach for predicting protein subcellular localization and achieved a satisfactory result; furthermore, we believe Esub8 will be a useful tool for predicting protein subcellular localizations in eukaryotic organisms

Multi-Scale Expressions of One Optimal State Regulated by Dopamine in the Prefrontal Cortex

The prefrontal cortex (PFC), which plays key roles in many higher cognitive processes, is a hierarchical system consisting of multi-scale organizations. Optimizing the working state at each scale is essential for PFC's information processing. Typical optimal working states at different scales have been separately reported, including the dopamine-mediated inverted-U profile of the working memory (WM) at the system level, critical dynamics at the network level, and detailed balance of excitatory and inhibitory currents (E/I balance) at the cellular level. However, it remains unclear whether these states are scale-specific expressions of the same optimal state and, if so, what is the underlying mechanism for its regulation traversing across scales. Here, by studying a neural network model, we show that the optimal performance of WM co-occurs with the critical dynamics at the network level and the E/I balance at the level of individual neurons, suggesting the existence of a unified, multi-scale optimal state for the PFC. Importantly, such a state could be modulated by dopamine at the synaptic level through a series of U or inverted-U profiles. These results suggest that seemingly different optimal states for specific scales are multi-scale expressions of one condition regulated by dopamine. Our work suggests a cross-scale perspective to understand the PFC function and its modulation

Functional connectivity in healthy subjects is nonlinearly modulated by the COMT and DRD2 polymorphisms in a functional system-dependent manner

The dopamine system is known to modulate brain function in an inverted U-shaped manner. Recently, the functional networks of the brain were categorized into two systems, a "control system" and a "processing system." However, it remains unclear whether the inverted U-shaped model of dopaminergic modulation could be applied to both of these functional systems. The catechol-O-methyltransferase (COMT) and dopamine D2 receptor (DRD2) were genotyped in 258 healthy young human subjects. The local and long-range functional connectivity densities (FCDs) of each voxel were calculated and compared in a voxel-wise manner using a two-way (COMT and DRD2 genotypes) analysis of covariance. The resting-state functional connectivity analysis was performed to determine the functional networks to which brain regions with significant FCD differences belonged. Significant COMT × DRD2 interaction effects were found in the local FCDs of the superior portion of the right temporal pole (sTP) and left lingual gyrus (LG) and in the long-range FCDs of the right putamen and left medial prefrontal cortex (MPFC). Post hoc tests showed nonlinear relationships between the genotypic subgroups and FCD. In the control system, the sTP and putamen, components of the salience network, showed a U-shaped modulation by dopamine signaling. In the processing system, however, the MPFC of the default-mode network and the LG of the visual network showed an inverted U-shaped modulation by the dopamine system. Our findings suggest an interaction between COMT and DRD2 genotypes and show a functional system-dependent modulation of dopamine signaling

Parcellation of the primary cerebral cortices based on local connectivity profiles

Connectivity-based parcellation using diffusion MRI has been extensively used to parcellate subcortical areas and the association cortex. Connectivity profiles are vital for connectivity-based parcellation. Two categories of connectivity profiles are generally utilized, including global connectivity profiles, in which the connectivity information is from the seed to the whole brain, and long connectivity profiles, in which the connectivity information is from the seed to other brain regions after excluding the seed. However, whether global or long connectivity profiles should be applied in parcellating the primary cortex utilizing connectivity-based parcellation is unclear. Many sources of evidence have indicated that the primary cerebral cortices are composed of structurally and functionally distinct subregions. Because the primary cerebral cortices are rich in local anatomic hierarchical connections and possess high degree of local functional connectivity profiles, we proposed that local connectivity profiles, that is the connectivity information within a seed region of interest, might be used for parcellating the primary cerebral cortices. In this study, the global, long, and local connectivity profiles were separately used to parcellate the bilateral M1, A1, S1, and V1. We found that results using the three profiles were all quite consistent with reported cytoarchitectonic evidence. More importantly, the results using local connectivity profiles showed less inter-subject variability than the results using the other two, a finding which suggests that local connectivity profiles are superior to global and long connectivity profiles for parcellating the primary cerebral cortices. This also implies that, depending on the characteristics of specific areas of the cerebral cortex, different connectivity profiles may need to be adopted to parcellate different areas