Morphological Neuron Classification Based on Dendritic Tree Hierarchy.

The shape of a neuron can reveal interesting properties about its function. Therefore, morphological neuron characterization can contribute to a better understanding of how the brain works. However, one of the great challenges of neuroanatomy is the definition of morphological properties that can be used for categorizing neurons. This paper proposes a new methodology for neuron morphological analysis by considering different hierarchies of the dendritic tree for characterizing and categorizing neuronal cells. The methodology consists in using different strategies for decomposing the dendritic tree along its hierarchies, allowing the identification of relevant parts (possibly related to specific neuronal functions) for classification tasks. A set of more than 5000 neurons corresponding to 10 classes were examined with supervised classification algorithms based on this strategy. It was found that classification accuracies similar to those obtained by using whole neurons can be achieved by considering only parts of the neurons. Branches close to the soma were found to be particularly relevant for classification.

Effects of threshold on the topology of gene co-expression networks.

Several developments regarding the analysis of gene co-expression profiles using complex network theory have been reported recently. Such approaches usually start with the construction of an unweighted gene co-expression network, therefore requiring the selection of a suitable threshold defining which pairs of vertices will be connected. We aimed at addressing such an important problem by suggesting and comparing five different approaches for threshold selection. Each of the methods considers a respective biologically-motivated criterion for electing a potentially suitable threshold. A set of 21 microarray experiments from different biological groups was used to investigate the effect of applying the five proposed criteria to several biological situations. For each experiment, we used the Pearson correlation coefficient to measure the relationship between each gene pair, and the resulting weight matrices were thresholded considering several values, generating respective adjacency matrices (co-expression networks). Each of the five proposed criteria was then applied in order to select the respective threshold value. The effects of these thresholding approaches on the topology of the resulting networks were compared by using several measurements, and we verified that, depending on the database, the impact on the topological properties can be large. However, a group of databases was verified to be similarly affected by most of the considered criteria. Based on such results, it can be suggested that when the generated networks present similar measurements, the thresholding method can be chosen with greater freedom. If the generated networks are markedly different, the thresholding method that better suits the interests of each specific research study represents a reasonable choice.

A framework for analyzing the relationship between gene expression and morphological, topological, and dynamical patterns in neuronal networks.

BACKGROUND: A key point in developmental biology is to understand how gene expression influences the morphological and dynamical patterns that are observed in living beings. NEW METHOD: In this work we propose a methodology capable of addressing this problem that is based on estimating the mutual information and Pearson correlation between the intensity of gene expression and measurements of several morphological properties of the cells. A similar approach is applied in order to identify effects of gene expression over the system dynamics. Neuronal networks were artificially grown over a lattice by considering a reference model used to generate artificial neurons. The input parameters of the artificial neurons were determined according to two distinct patterns of gene expression and the dynamical response was assessed by considering the integrate-and-fire model. RESULTS: As far as single gene dependence is concerned, we found that the interaction between the gene expression and the network topology, as well as between the former and the dynamics response, is strongly affected by the gene expression pattern. In addition, we observed a high correlation between the gene expression and some topological measurements of the neuronal network for particular patterns of gene expression. COMPARISON WITH EXISTING METHODS: To our best understanding, there are no similar analyses to compare with. CONCLUSIONS: A proper understanding of gene expression influence requires jointly studying the morphology, topology, and dynamics of neurons. The proposed framework represents a first step towards predicting gene expression patterns from morphology and connectivity.

An image processing approach to analyze morphological features of microscopic images of muscle fibers.

We present an image processing approach to automatically analyze duo-channel microscopic images of muscular fiber nuclei and cytoplasm. Nuclei and cytoplasm play a critical role in determining the health and functioning of muscular fibers as changes of nuclei and cytoplasm manifest in many diseases such as muscular dystrophy and hypertrophy. Quantitative evaluation of muscle fiber nuclei and cytoplasm thus is of great importance to researchers in musculoskeletal studies. The proposed computational approach consists of steps of image processing to segment and delineate cytoplasm and identify nuclei in two-channel images. Morphological operations like skeletonization is applied to extract the length of cytoplasm for quantification. We tested the approach on real images and found that it can achieve high accuracy, objectivity, and robustness.

A systematic comparison of supervised classifiers.

Pattern recognition has been employed in a myriad of industrial, commercial and academic applications. Many techniques have been devised to tackle such a diversity of applications. Despite the long tradition of pattern recognition research, there is no technique that yields the best classification in all scenarios. Therefore, as many techniques as possible should be considered in high accuracy applications. Typical related works either focus on the performance of a given algorithm or compare various classification methods. In many occasions, however, researchers who are not experts in the field of machine learning have to deal with practical classification tasks without an in-depth knowledge about the underlying parameters. Actually, the adequate choice of classifiers and parameters in such practical circumstances constitutes a long-standing problem and is one of the subjects of the current paper. We carried out a performance study of nine well-known classifiers implemented in the Weka framework and compared the influence of the parameter configurations on the accuracy. The default configuration of parameters in Weka was found to provide near optimal performance for most cases, not including methods such as the support vector machine (SVM). In addition, the k-nearest neighbor method frequently allowed the best accuracy. In certain conditions, it was possible to improve the quality of SVM by more than 20% with respect to their default parameter configuration.

Shape, connectedness and dynamics in neuronal networks.

The morphology of neurons is directly related to several aspects of the nervous system, including its connectedness, health, development, evolution, dynamics and, ultimately, behavior. Such interplays of the neuronal morphology can be understood within the more general shape-function paradigm. The current article reviews, in an introductory way, some key issues regarding the role of neuronal morphology in the nervous system, with emphasis on works developed in the authors' group. The following topics are addressed: (a) characterization of neuronal shape; (b) stochastic synthesis of neurons and neuronal systems; (c) characterization of the connectivity of neuronal networks by using complex networks concepts; and (d) investigations of influences of neuronal shape on network dynamics. The presented concepts and methods are useful also for several other multiple object systems, such as protein-protein interaction, tissues, aggregates and polymers.

A methodology to infer gene networks from spatial patterns of expression--an application to fluorescence in situ hybridization images.

The proper functional development of a multicellular organism depends on an intricate network of interacting genes that are expressed in accurate temporal and spatial patterns across different tissues. Complex inhibitory and excitatory interactions among genes control the territorial differences that explain specialized cell fates, embryo polarization and tissues architecture in metazoans. Given the nature of the regulatory gene networks, similarity of expression patterns can identify genes with similar roles. The inference and analysis of the gene interaction networks through complex network tools can reveal important aspects of the biological system modeled. Here we suggest an image analysis pipeline to quantify co-localization patterns in in situ hybridization images of Drosophila embryos and, based on these patterns, infer gene networks. We analyze the spatial dispersion of the gene expression and show the gene interaction networks for different developmental stages. Our results suggest that the inference of developmental networks based on spatial expression data is biologically relevant and represents a potential tool for the understanding of animal development.

Identifying the starting point of a spreading process in complex networks.

When dealing with the dissemination of epidemics, one important question that can be asked is the location where the contamination began. In this paper, we analyze three spreading schemes and propose and validate an effective methodology for the identification of the source nodes. The method is based on the calculation of the centrality of the nodes on the sampled network, expressed here by degree, betweenness, closeness, and eigenvector centrality. We show that the source node tends to have the highest measurement values. The potential of the methodology is illustrated with respect to three theoretical complex network models as well as a real-world network, the email network of the University Rovira i Virgili.