Discriminating shape descriptors based on connectivity

We propose a method for enhancing the accuracy of shape descriptors. The concept of connectivity to obtain discriminating shape descriptors, is introduced. We show how connectivity is applied to two popular shape descriptors. Experiments are performed to test the effect of using connectivity with generic Fourier descriptors and distance histograms. Item S8 within the MPEG-7 still images content set is used for performing experiments. This dataset consists of 3621 still images. The experimental results show that connectivity enhances the performance of the methods significantly. <br /

Multi-scale analysis of connectivity for image retrieval

Previously, we proposed the concept of connectivity to obtain discriminating shape descriptors. In this paper, we use connectivity to obtain superior distance histograms for multi-scale images. Experiments are performed to evaluate the distance histograms, based on connectivity, for shape-based retrieval of multi-scale images. Item S8 within the MPEG-7 still images content set is used for performing experiments. Experimental results show that the proposed method enhances retrieval performance significantly.<br /

Characterizing neuromorphologic alterations with additive shape functionals

The complexity of a neuronal cell shape is known to be related to its function. Specifically, among other indicators, a decreased complexity in the dendritic trees of cortical pyramidal neurons has been associated with mental retardation. In this paper we develop a procedure to address the characterization of morphological changes induced in cultured neurons by over-expressing a gene involved in mental retardation. Measures associated with the multiscale connectivity, an additive image functional, are found to give a reasonable separation criterion between two categories of cells. One category consists of a control group and two transfected groups of neurons, and the other, a class of cat ganglionary cells. The reported framework also identified a trend towards lower complexity in one of the transfected groups. Such results establish the suggested measures as an effective descriptors of cell shape

Corners-based composite descriptor for shapes

In this paper, a composite descriptor for shape retrieval is proposed. The composite descriptor is obtained based upon corner-points and shape region. In an earlier paper, we proposed a composite descriptor based on shape region and shape contour, however, the descriptor was not effective for all perspective and geometric transformations. Hence, we modify the composite descriptor by replacing contour features with corner-points features. The proposed descriptor is obtained from Generic FourierDescriptors (GFD) of the shape region and the GFD ofthe corner-points. We study the performance of the proposed composite descriptor. The proposed method is evaluated using Item S8 within the MPEG-7 Still Images Content Set. Experimental results show that the proposed descriptor is effective.<br /

The Cluster Distribution as a Test of Dark Matter Models. IV: Topology and Geometry

We study the geometry and topology of the large-scale structure traced by galaxy clusters in numerical simulations of a box of side 320 $h^{-1}$ Mpc, and compare them with available data on real clusters. The simulations we use are generated by the Zel'dovich approximation, using the same methods as we have used in the first three papers in this series. We consider the following models to see if there are measurable differences in the topology and geometry of the superclustering they produce: (i) the standard CDM model (SCDM); (ii) a CDM model with $\Omega_0=0.2$ (OCDM); (iii) a CDM model with a `tilted' power spectrum having $n=0.7$ (TCDM); (iv) a CDM model with a very low Hubble constant, $h=0.3$ (LOWH); (v) a model with mixed CDM and HDM (CHDM); (vi) a flat low-density CDM model with $\Omega_0=0.2$ and a non-zero cosmological $\Lambda$ term ($\Lambda$CDM). We analyse these models using a variety of statistical tests based on the analysis of: (i) the Euler-Poincar\'{e} characteristic; (ii) percolation properties; (iii) the Minimal Spanning Tree construction. Taking all these tests together we find that the best fitting model is $\Lambda$CDM and, indeed, the others do not appear to be consistent with the data. Our results demonstrate that despite their biased and extremely sparse sampling of the cosmological density field, it is possible to use clusters to probe subtle statistical diagnostics of models which go far beyond the low-order correlation functions usually applied to study superclustering.Comment: 17 pages, 7 postscript figures, uses mn.sty, MNRAS in pres

Applications of Minkowski Functionals to the Statistical Analysis of Dark Matter Models

A new method for the statistical analysis of 3D point processes, based on the family of Minkowski functionals, is explained and applied to modelled galaxy distributions generated by a toy-model and cosmological simulations of the large-scale structure in the Universe. These measures are sensitive to both, geometrical and topological properties of spatial patterns and appear to be very effective in discriminating different point processes. Moreover by the means of conditional subsampling, different building blocks of large-scale structures like sheets, filaments and clusters can be detected and extracted from a given distribution.Comment: 13 pages, Latex, 2 gzipped tar-files, to appear in: Proc. ``1st SFB workshop on Astro-particle physics'', Ringberg, Tegernsee, 199

Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces

© 2016 Kontopoulos et al.Background: The term molecular cartography encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorithms comprise multiple manual steps, whereas the few existing implementations typically restrict the user to a very limited set of molecular descriptors. Results: We present Structuprint, a free standalone software that fully automates the rendering of protein surface maps, given - at the very least - a directory with a PDB file and an amino acid property. The tool comes with a default database of 328 descriptors, which can be extended or substituted by user-provided ones. The core algorithm comprises the generation of a mould of the protein surface, which is subsequently converted to a sphere and mapped to two dimensions, using the Miller cylindrical projection. Structuprint is partly optimized for multicore computers, making the rendering of animations of entire molecular dynamics simulations feasible. Conclusions: Structuprint is an efficient application, implementing a molecular cartography algorithm for protein surfaces. According to the results of a benchmark, its memory requirements and execution time are reasonable, allowing it to run even on low-end personal computers. We believe that it will be of use - primarily but not exclusively - to structural biologists and computational biochemists

Infinite Feature Selection on Shore-Based Biomarkers Reveals Connectivity Modulation after Stroke

Connectomics is gaining increasing interest in the scientific and clinical communities. It consists in deriving models of structural or functional brain connections based on some local measures. Here we focus on structural connectivity as detected by diffusion MRI. Connectivity matrices are derived from microstructural indices obtained by the 3D-SHORE. Typically, graphs are derived from connectivity matrices and used for inferring node properties that allow identifying those nodes that play a prominent role in the network. This information can then be used to detect network modulations induced by diseases. In this paper we take a complementary approach and focus on link as opposed to node properties. We hypothesize that network modulation can be better described by measuring the connectivity alteration directly in the form of modulation of the properties of white matter fiber bundles constituting the network communication backbone. The goal of this paper is to detect the paths that are most altered by the pathology by exploiting a feature selection paradigm. Temporal changes on connection weights are treated as features and those playing a leading role in a patient versus healthy controls classification task are detected by the Infinite Feature Selection (Inf-FS) method. Results show that connection paths with high discriminative power can be identified that are shared by the considered microstructural descriptors allowing a classification accuracy ranging between 83% and 89%