Thick Line Segment Detection with Fast Directional Tracking

International audienceThis paper introduces a fully discrete framework for a new straight line detector in gray-level images, where line segments are enriched with a thickness parameter intended to provide a quality criterion on the extracted feature. This study is based on a previous work on interactive line detection in gray-level images. At first, a better estimation of the segment thickness and orientation is achieved through two main improvements: adaptive directional scans and control of assigned thickness. Then, these advances are exploited for a complete unsupervised detection of all the line segments in an image. The new thick line detector is left available in an online demonstration

SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics

<p>Abstract</p> <p>Background</p> <p>Many programs have been developed to identify transcription factor binding sites. However, most of them are not able to infer two-word motifs with variable spacer lengths. This case is encountered for RNA polymerase Sigma (<it>σ</it>) Factor Binding Sites (SFBSs) usually composed of two boxes, called -35 and -10 in reference to the transcription initiation point. Our goal is to design an algorithm detecting SFBS by using combinational and statistical constraints deduced from biological observations.</p> <p>Results</p> <p>We describe a new approach to identify SFBSs by comparing two related bacterial genomes. The method, named SIGffRid (SIGma Factor binding sites Finder using R'MES to select Input Data), performs a simultaneous analysis of pairs of promoter regions of orthologous genes. SIGffRid uses a prior identification of over-represented patterns in whole genomes as selection criteria for potential -35 and -10 boxes. These patterns are then grouped using pairs of short seeds (of which one is possibly gapped), allowing a variable-length spacer between them. Next, the motifs are extended guided by statistical considerations, a feature that ensures a selection of motifs with statistically relevant properties. We applied our method to the pair of related bacterial genomes of <it>Streptomyces coelicolor </it>and <it>Streptomyces avermitilis</it>. Cross-check with the well-defined SFBSs of the SigR regulon in <it>S. coelicolor </it>is detailed, validating the algorithm. SFBSs for HrdB and BldN were also found; and the results suggested some new targets for these <it>σ </it>factors. In addition, consensus motifs for BldD and new SFBSs binding sites were defined, overlapping previously proposed consensuses. Relevant tests were carried out also on bacteria with moderate GC content (i.e. <it>Escherichia coli</it>/<it>Salmonella typhimurium </it>and <it>Bacillus subtilis</it>/<it>Bacillus licheniformis </it>pairs). Motifs of house-keeping <it>σ </it>factors were found as well as other SFBSs such as that of SigW in <it>Bacillus </it>strains.</p> <p>Conclusion</p> <p>We demonstrate that our approach combining statistical and biological criteria was successful to predict SFBSs. The method versatility autorizes the recognition of other kinds of two-box regulatory sites.</p

SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics

<p>Abstract</p> <p>Background</p> <p>Many programs have been developed to identify transcription factor binding sites. However, most of them are not able to infer two-word motifs with variable spacer lengths. This case is encountered for RNA polymerase Sigma (<it>σ</it>) Factor Binding Sites (SFBSs) usually composed of two boxes, called -35 and -10 in reference to the transcription initiation point. Our goal is to design an algorithm detecting SFBS by using combinational and statistical constraints deduced from biological observations.</p> <p>Results</p> <p>We describe a new approach to identify SFBSs by comparing two related bacterial genomes. The method, named SIGffRid (SIGma Factor binding sites Finder using R'MES to select Input Data), performs a simultaneous analysis of pairs of promoter regions of orthologous genes. SIGffRid uses a prior identification of over-represented patterns in whole genomes as selection criteria for potential -35 and -10 boxes. These patterns are then grouped using pairs of short seeds (of which one is possibly gapped), allowing a variable-length spacer between them. Next, the motifs are extended guided by statistical considerations, a feature that ensures a selection of motifs with statistically relevant properties. We applied our method to the pair of related bacterial genomes of <it>Streptomyces coelicolor </it>and <it>Streptomyces avermitilis</it>. Cross-check with the well-defined SFBSs of the SigR regulon in <it>S. coelicolor </it>is detailed, validating the algorithm. SFBSs for HrdB and BldN were also found; and the results suggested some new targets for these <it>σ </it>factors. In addition, consensus motifs for BldD and new SFBSs binding sites were defined, overlapping previously proposed consensuses. Relevant tests were carried out also on bacteria with moderate GC content (i.e. <it>Escherichia coli</it>/<it>Salmonella typhimurium </it>and <it>Bacillus subtilis</it>/<it>Bacillus licheniformis </it>pairs). Motifs of house-keeping <it>σ </it>factors were found as well as other SFBSs such as that of SigW in <it>Bacillus </it>strains.</p> <p>Conclusion</p> <p>We demonstrate that our approach combining statistical and biological criteria was successful to predict SFBSs. The method versatility autorizes the recognition of other kinds of two-box regulatory sites.</p

Blurred Segments in Gray Level Images for Interactive Line Extraction

International audienceAbstract. The recognition of discrete straight segments is a significant topic in the field of discrete geometry and for many applications dealing with geometric feature extraction. It can be performed from noisy binary data using the concept of blurred segments [3,2]. However, to our best knowledge, these algorithms have never been defined to directly extract straight segments in gray level images. This article proposes a solution to extend the recognition by using gray level image information. Although initially intended to be implemented within a semi-automatic line selec- tion tool used in an interactive 3D modeling application, it also meets more general parameter extraction requirements

Convexity-preserving rigid motions of 2D digital objects

International audienceRigid motions on R^2 are isometric and thus preserve the geometry and topology of objects. However, this important property is generally lost when considering digital objects defined on Z^2 , due to the digitization process from R^2 to Z^2. In this article, we focus on the convexity property of digital objects, and propose an approach for rigid motions of digital objects which preserves this convexity. The method is extended to non-convex objects, based on the concavity tree representation

Author manuscript, published in &quot;CompIMAGE, Buffalo-Niagara: États-Unis (2010)&quot; Curvature Estimation for Discrete Curves Based on Auto-adaptive Masks of Convolution

Abstract. We propose a method that we call auto-adaptive convolution which extends the classical notion of convolution in pictures analysis to function analysis on a discrete set. We define an averaging kernel which takes into account the local geometry of a discrete shape and adapts itself to the curvature. Its defining property is to be local and to follow a normal law on discrete lines of any slope. We used it together with classical differentiation masks to estimate first and second derivatives and give a curvature estimator of discrete functions.

Parallel Strip Segment Recognition and Application to Metallic Tubular Object Measure

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Normals and Curvature Estimation for Digital Surfaces Based on Convolutions

International audienceIn this paper, we present a method that we call on-surface convolution which extends the classical notion of a 2D digital filter to the case of digital surfaces (following the cuberille model). We also define an averaging mask with local support which, when applied with the iterated convolution operator, behaves like an averaging with large support. The interesting property of the latter averaging is the way the resulting weights are distributed: they tend to decrease following a “continuous” geodesic distance within the surface. We eventually use the iterated averaging followed by convolutions with differentiation masks to estimate partial derivatives and then normal vectors over a surface. We provide an heuristics based on [14] for an optimal mask size and show results