Writing Reusable Digital Geometry Algorithms in a Generic Image Processing Framework

Digital Geometry software should reflect the generality of the underlying mathe- matics: mapping the latter to the former requires genericity. By designing generic solutions, one can effectively reuse digital geometry data structures and algorithms. We propose an image processing framework focused on the Generic Programming paradigm in which an algorithm on the paper can be turned into a single code, written once and usable with various input types. This approach enables users to design and implement new methods at a lower cost, try cross-domain experiments and help generalize resultsComment: Workshop on Applications of Discrete Geometry and Mathematical Morphology, Istanb : France (2010

Cellular Skeletons: A New Approach to Topological Skeletons with Geometric Features

This paper introduces a new kind of skeleton for binary volumes called the cellular skeleton. This skeleton is not a subset of voxels of a volume nor a subcomplex of a cubical complex: it is a chain complex together with a reduction from the original complex. Starting from the binary volume we build a cubical complex which represents it regarding 6 or 26-connectivity. Then the complex is thinned using the proposed method based on elementary collapses, which preserves significant geometric features. The final step reduces the number of cells using Discrete Morse Theory. The resulting skeleton is a reduction which preserves the homology of the original complex and the geometrical information of the output of the previous step. The result of this method, besides its skeletonization content, can be used for computing the homology of the original complex, which usually provides well shaped homology generators

Description of the topographical changes associated to the different stages of the DsbA catalytic cycle.

This paper provides a description of the surface topography of DsbA, the bacterial disulfide-bond forming enzyme, in the different phases of its catalytic cycle. Three representative states, that is, oxidized and reduced protein and a covalent complex mimicking the DsbA-substrate disulfide intermediate, have been investigated by a combination of limited proteolysis experiments and mass spectrometry methodologies. Protease-accessible sites are largely distributed in the oxidized form with a small predominance inside the thioredoxin domain. Proteolysis occurs even in secondary structure elements, revealing a significant mobility of the protein. Many cleavage sites disappear in the reduced form and most of the remaining ones appear with strongly reduced kinetics. The protein within the complex shows an intermediate behavior. This variation of flexibility in DsbA is probably the determining factor for the course of its catalytic cycle. In particular, the great mobility of the oxidized protein might facilitate the accommodation of its various substrates, whereas the increasing rigidity from the complexed to the reduced form could help the release of oxidized products. The formation of the complex between PID peptide and DsbA does not significantly protect the enzyme against proteolysis, reinforcing the results previously obtained by calorimetry concerning the weakness of their interaction. The few cleavage sites observed, however, are in favor of the presence of the peptide in the binding site postulated from crystallographic studies. As for the peptide itself, the proteolytic pattern and the protection effect exerted by DsbA could be explained by a preferential orientation within the binding site

On the equivalence between hierarchical segmentations and ultrametric watersheds

We study hierarchical segmentation in the framework of edge-weighted graphs. We define ultrametric watersheds as topological watersheds null on the minima. We prove that there exists a bijection between the set of ultrametric watersheds and the set of hierarchical segmentations. We end this paper by showing how to use the proposed framework in practice in the example of constrained connectivity; in particular it allows to compute such a hierarchy following a classical watershed-based morphological scheme, which provides an efficient algorithm to compute the whole hierarchy.Comment: 19 pages, double-colum

Fully Parallel Hyperparameter Search: Reshaped Space-Filling

Space-filling designs such as scrambled-Hammersley, Latin Hypercube Sampling and Jittered Sampling have been proposed for fully parallel hyperparameter search, and were shown to be more effective than random or grid search. In this paper, we show that these designs only improve over random search by a constant factor. In contrast, we introduce a new approach based on reshaping the search distribution, which leads to substantial gains over random search, both theoretically and empirically. We propose two flavors of reshaping. First, when the distribution of the optimum is some known $P_0$, we propose Recentering, which uses as search distribution a modified version of $P_0$ tightened closer to the center of the domain, in a dimension-dependent and budget-dependent manner. Second, we show that in a wide range of experiments with $P_0$ unknown, using a proposed Cauchy transformation, which simultaneously has a heavier tail (for unbounded hyperparameters) and is closer to the boundaries (for bounded hyperparameters), leads to improved performances. Besides artificial experiments and simple real world tests on clustering or Salmon mappings, we check our proposed methods on expensive artificial intelligence tasks such as attend/infer/repeat, video next frame segmentation forecasting and progressive generative adversarial networks

Average Curve of n Digital Curves

International audienc

Constructive links between some morphological hierarchies on edge-weighted graphs

International audienceIn edge-weighted graphs, we provide a unified presentation of a family of popular morphological hierarchies such as component trees, quasi flat zones, binary partition trees, and hierarchical watersheds. For any hierarchy of this family, we show if (and how) it can be obtained from any other element of the family. In this sense, the main contribution of this paper is the study of all constructive links between these hierarchies

A Compact Ring for Thom X-Ray Source

International audienceThe goal of X-ray sources based on Compton back scattering processes is to develop a compact device, which could produce an intense flux of monochromatic X-rays. Compton back-scattering resuls from collisions between laser pulses and relativistic electron bunches. Due to the relative low value of the Compton cross section, a high charge electron beam, a low emittance and a high focusing at the interaction point are required for the electron beam. In addition, the X-ray flux is related to the characteristics of the electron beam, which are themselves dynamically affected by the Compton interaction. One possible configuration is to inject frequently into a storage ring with a low emittance linear accelerator without waiting for the synchrotron equilibrium. As a consequence, the optics should be designed taking into account the characteristics of the electron beam from the linear accelerator. The accelerator ring design for a 50 MeV electron beam, aiming at producing a flux higher than 1013 ph/s, will be presented

Liver segmentation in MRI: a fully automatic method based on stochastic partitions

There are few fully automated methods for liver segmentation in magnetic resonance images (MRI) despite the benefits of this type of acquisition in comparison to other radiology techniques such as computed tomography (CT). Motivated by medical requirements, liver segmentation in MRI has been carried out. For this purpose, we present a new method for liver segmentation based on the watershed transform and stochastic partitions. The classical watershed over-segmentation is reduced using a marker-controlled algorithm. To improve accuracy of selected contours, the gradient of the original image is successfully enhanced by applying a new variant of stochastic watershed. Moreover, a final classifier is performed in order to obtain the final liver mask. Optimal parameters of the method are tuned using a training dataset and then they are applied to the rest of studies (17 datasets). The obtained results (a Jaccard coefficient of 0.91 +/- 0.02) in comparison to other methods demonstrate that the new variant of stochastic watershed is a robust tool for automatic segmentation of the liver in MRI. (C) 2014 Elsevier Ireland Ltd. All rights reserved.This work has been supported by the MITYC under the project NaRALap (ref. TSI-020100-2009-189), partially by the CDTI under the project ONCOTIC (IDI-20101153), by Ministerio de Educacion y Ciencia Spain, Project Game Teen (TIN2010-20187) projects Consolider-C (SEJ2006-14301/PSIC), "CIBER of Physiopathology of Obesity and Nutrition, an initiative of ISCIII" and Excellence Research Program PROMETEO (Generalitat Valenciana. Conselleria de Educacion, 2008-157). We would like to express our gratitude to the Hospital Clinica Benidorm, for providing the MR datasets and to the radiologist team of Inscanner for the manual segmentation of the MR images.López-Mir, F.; Naranjo Ornedo, V.; Angulo, J.; Alcañiz Raya, ML.; Luna, L. (2014). Liver segmentation in MRI: a fully automatic method based on stochastic partitions. Computer Methods and Programs in Biomedicine. 114(1):11-28. https://doi.org/10.1016/j.cmpb.2013.12.022S1128114