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

Unsupervised Polygonal Reconstruction of Noisy Contours by a Discrete Irregular Approach

International audienceIn this paper, we present an original algorithm to build a polygonal reconstruction of noisy digital contours. For this purpose, we first improve an algorithm devoted to the vectorization of discrete irregular isothetic objects. Afterwards we propose to use it to define a reconstruction process of noisy digital contours. More precisely, we use a local noise detector, introduced by Kerautret and Lachaud in IWCIA 2009, that builds a multi-scale representation of the digital contour, which is composed of pixels of various size depending of the local amount of noise. Finally, we compare our approach with previous works, by con- sidering the Hausdorff distance and the error on tangent orientations of the computed line segments to the original perfect contour. Thanks to both synthetic and real noisy objects, we show that our approach has interesting performance, and could be applied in document analysis systems

Average Curve of n Digital Curves

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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

Algorithms for Fast Digital Straight Segments Union

International audienceGiven two Digital Straight Segments (DSS for short) of known minimal characteristics, we investigate the union of these DSSs: is it still a DSS ? If yes, what are its minimal characteristics ? We show that the problem is actually easy and can be solved in, at worst, logarithmic time using a state-of-the-art algorithm. We moreover propose a new algorithm of logarithmic worst-case complexity based on arithmetical properties. But when the two DSSs are connected, the time complexity of this algorithm is lowered to O(1) and experiments show that it outperforms the state-of-the art one in any case

I.: Geometric feature estimators for noisy discrete surfaces

Abstract. We present in this paper robust geometric feature estimators on the border of a possibly noisy discrete object. We introduce the notion of patch centered at a point of this border. Thanks to a width parameter, attached to a patch, the noise on the border of the discrete object can be considered, and an extended flat neighborhood of a border point is computed. Stable geometric features are then extracted around this point. A normal vector estimator is proposed as well as a detector of convex and concave parts on the border of a discrete object.

Multilevel Polygonal Descriptor Matching Defined By Combining Discrete Lines And Force Histogram Concepts

International audienceA new method allowing to describe shapes from a set of polygonal curves using a relational descriptor is proposed in this paper. An approach based on discrete lines at several increasing widths is run on the contour of an object to provide a multi-level polygonal representation from accurate description to more and more rough aspects. On each polygon is calculated a force histogram to define a relational feature signature following a set of directions integrating both spatial relation organization and disparities of the shape in a same distribution. Three different matching schemes are proposed to compare multilevel distributions: global representation, level to level following extracted maxima. This new method is fast and a first experimental study achieved on a common database shows its good behavior