Automatic quantitative evaluation of image registration techniques with the "epsilon" dissimilarity criterion in the case of retinal images.

International audienceIn human retina observation (with non mydriatic optical microscopes), a registration process is often employed to enlarge the field of view. For the ophthalmologist, this is a way to spare time browsing all the images. A lot of techniques have been proposed to perform this registration process, and indeed, its good evaluation is a question that can be raised. This article presents the use of the "epsilon" dissimilarity criterion to evaluate and compare some classical featurebased image registration techniques. The problem of retina images registration is employed as an example, but it could also be used in other applications. The images are first segmented and these segmentations are registered. The good quality of this registration is evaluated with the "epsilon" dissimilarity criterion for 25 pairs of images with a manual selection of control points. This study can be useful in order to choose the type of registration method and to evaluate the results of a new one

A feature-based dense local registration of pairs of retinal images.

International audienceA method for spatial registering pairs of digital images of the retina is presented, using intrinsic feature points (landmarks) and dense local transformation. First, landmarks, i.e. blood vessel bifurcations, are extracted from both retinal images using filtering followed by thinning and branch point analysis. Correspondances are found by topological and structural comparisons between both retinal networks. From this set of matching points, a displacement field is computed and, finally, one of the two images is transformed. Due to complex retinal registration problem, the presented transformation is dense, local and adaptive. Experimental results established the effectiveness and the interest of the dense registration method

Quantitative evaluation of image registration techniques in the case of retinal images

International audienceIn human retina observation (with non mydriatic optical microscopes), an image registration process is often employed to enlarge the field of view. Analyzing all the images takes a lot of time. Numerous techniques have been proposed to perform the registration process. Its good evaluation is a difficult question that is then raising. This article presents the use of two quantitative criterions to evaluate and compare some classical feature-based image registration techniques. The images are first segmented and the resulting binary images are then registered. The good quality of the registration process is evaluated with a normalized criterion based on the ϵ dissimilarity criterion, and the figure of merit criterion (fom), for 25 pairs of images with a manual selection of control points. These criterions are normalized by the results of the affine method (considered as the most simple method). Then, for each pair, the influence of the number of points used to perform the registration is evaluated

Poisson homology of r-matrix type orbits I: example of computation

In this paper we consider the Poisson algebraic structure associated with a classical $r$-matrix, i.e. with a solution of the modified classical Yang--Baxter equation. In Section 1 we recall the concept and basic facts of the $r$-matrix type Poisson orbits. Then we describe the $r$-matrix Poisson pencil (i.e the pair of compatible Poisson structures) of rank 1 or $CP^n$-type orbits of $SL(n,C)$. Here we calculate symplectic leaves and the integrable foliation associated with the pencil. We also describe the algebra of functions on $CP^n$-type orbits. In Section 2 we calculate the Poisson homology of Drinfeld--Sklyanin Poisson brackets which belong to the $r$-matrix Poisson family

Integration of Holomorphic Lie Algebroids

We prove that a holomorphic Lie algebroid is integrable if, and only if, its underlying real Lie algebroid is integrable. Thus the integrability criteria of Crainic-Fernandes do also apply in the holomorphic context without any modification. As a consequence we give another proof of the following theorem: a holomorphic Poisson manifold is integrable if, and only if, its real (or imaginary) part is integrable as a real Poisson manifold.Comment: 26 pages, second part of arXiv:0707.4253 which was split into two, v2: example 3.19 and section 3.7 adde

Gene silencing based on RNA-guided catalytically inactive Cas9 (dCas9): a new tool for genetic engineering in Leptospira

International audienceLeptospirosis is a worldwide zoonosis caused by pathogenic bacteria of the genus Leptospira, which also includes free-living saprophyte strains. Many aspects of leptospiral basic biology and virulence mechanisms remain unexplored mainly due to the lack of effective genetic tools available for these bacteria. Recently, the type II CRISPR/Cas system from Streptococcus pyogenes has been widely used as an efficient genome engineering tool in bacteria by inducing double-strand breaks (DSBs) in the desired genomic targets caused by an RNA-guided DNA endonuclease called Cas9, and the DSB repair associated machinery. In the present work, plasmids expressing heterologous S. pyogenes Cas9 in L. biflexa cells were generated, and the enzyme could be expressed with no apparent toxicity to leptospiral cells. However, L. biflexa cells were unable to repair RNA-guided Cas9-induced DSBs. Thus, we used a catalytically dead Cas9 (dCas9) to obtain gene silencing rather than disruption, in a strategy called CRISPR interference (CRISPRi). We demonstrated complete gene silencing in L. biflexa cells when both dCas9 and single-guide RNA (sgRNA) targeting the coding strand of the β-galactosidase gene were expressed simultaneously. Furthermore, when the system was applied for silencing the dnaK gene, no colonies were recovered, indicating that DnaK protein is essential in Leptospira. In addition, flagellar motor switch FliG gene silencing resulted in reduced bacterial motility. To the best of our knowledge, this is the first work applying the CRISPRi system in Leptospira and spirochetes in general, expanding the tools available for understanding leptospiral biology

Effects of PI and PIII Snake Venom Haemorrhagic Metalloproteinases on the Microvasculature: A Confocal Microscopy Study on the Mouse Cremaster Muscle

The precise mechanisms by which Snake Venom Metalloproteinases (SVMPs) disrupt the microvasculature and cause haemorrhage have not been completely elucidated, and novel in vivo models are needed. In the present study, we compared the effects induced by BaP1, a PI SVMP isolated from Bothrops asper venom, and CsH1, a PIII SVMP from Crotalus simus venom, on cremaster muscle microvasculature by topical application of the toxins on isolated tissue (i.e., ex vivo model), and by intra-scrotal administration of the toxins (i.e., in vivo model). The whole tissue was fixed and immunostained to visualize the three components of blood vessels by confocal microscopy. In the ex vivo model, BaP1 was able to degrade type IV collagen and laminin from the BM of microvessels. Moreover, both SVMPs degraded type IV collagen from the BM in capillaries to a higher extent than in PCV and arterioles. CsH1 had a stronger effect on type IV collagen than BaP1. In the in vivo model, the effect of BaP1 on type IV collagen was widespread to the BM of arterioles and PCV. On the other hand, BaP1 was able to disrupt the endothelial barrier in PCV and to increase vascular permeability. Moreover, this toxin increased the size of gaps between pericytes in PCV and created new gaps between smooth muscle cells in arterioles in ex vivo conditions. These effects were not observed in the case of CsH1. In conclusion, our findings demonstrate that both SVMPs degrade type IV collagen from the BM in capillaries in vivo. Moreover, while the action of CsH1 is more directed to the BM of microvessels, the effects of BaP1 are widespread to other microvascular components. This study provides new insights in the mechanism of haemorrhage and other pathological effects induced by these toxins

Molecular dynamics simulations of sequence-defined oligomers for catalysis

Sequence-defined Polymers: Engineering Materials with Biological Precision - Fédération Wallonie Bruxelle

Molecular dynamics simulations of sequence-defined oligomers for catalysis

Sequence-defined Polymers: Engineering Materials with Biological Precision - Fédération Wallonie Bruxelle

Discrete Multifunctional Sequence-Defined Oligomers with Controlled Chirality

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