Implementation and Evaluation of Power Consumption of an Iris Pre-processing Algorithm on Modern FPGA

In this article, the efficiency and applicability of several power reduction techniques applied on a modern 65nm FPGA is described. For image erosion and dilation algorithms, two major solutions were tested and compared with respect to power and energy consumption. Firstly the algorithm was run on a general purpose processor (gpp) NIOS and then hardware architecture of an Intellectual Property (IP) was designed. Furthermore IPs design was improved by applying a number of power optimization techniques. They involved RTL level clock gating, power driven synthesis with fitting and appropriate coding style. Results show that hardware implementation is much more energy efficient than a general purpose processor and power optimization schemes can reduce the overall power consumption on an FPGA

Enhancement of Optical Coherence Tomography Images of the Retina by Normalization and Fusion

This paper describes an image processing method applied to Optical Coherence Tomography (OCT) images of the retina. The aim is to achieve improved OCT images from the fusion of sequential OCT scans obtained at identical retinal locations. The method is based on the normalization of the acquired images and their fusion. As a result, a noise reduction and an image enhancement are reached. Thanks to the resulting improvement in retinal imaging, clinical specialists are able to evaluate more efficiently eyes pathologies and anomalies. This paper presents the proposed method and gives some evaluation results

Amélioration de la reconnaissance de partitions musicales par modélisation floue et indication des erreurs possibles

Nous proposons une méthode de reconnaissance de partitions musicales fondée sur la modélisation floue des informations extraites de la partition scannée et des règles de musique. L'objectif est de prendre en compte les ambiguïtés qui subsistent à l'issue de l'étape d'analyse individuelle des symboles, et d'obtenir une interprétation globale cohérente. Le formalisme proposé permet de modéliser l'imprécision sur la détection des symboles, la variabilité des polices, la souplesse des règles musicales, et ainsi de fiabiliser les résultats de reconnaissance. Nous montrerons qu'il permet également d'indiquer les erreurs potentielles, de manière à faciliter la correction manuelle

Toward Guidelines for Research on Human Embryo Models Formed from Stem Cells.

Over the past few years, a number of research groups have reported striking progress on the generation of in vitro models from mouse and human stem cells that replicate aspects of early embryonic development. Not only do these models reproduce some key cell fate decisions but, especially in the mouse system, they also mimic the spatiotemporal arrangements of embryonic and extraembryonic tissues that are required for developmental patterning and implantation in the uterus. If such models could be developed for the early human embryo, they would have great potential benefits for understanding early human development, for biomedical science, and for reducing the use of animals and human embryos in research. However, guidelines for the ethical conduct of this line of work are at present not well defined. In this Forum article, we discuss some key aspects of this emerging area of research and provide some recommendations for its ethical oversight

Deep-learning based segmentation of challenging myelin sheaths

The segmentation of axons and myelin in electron microscopy images allows neurologists to highlight the density of axons and the thickness of the myelin surrounding them. These properties are of great interest for preventing and anticipating white matter diseases. This task is generally performed manually, which is a long and tedious process. We present an update of the methods used to compute that segmentation via machine learning. Our model is based on the architecture of the U-Net network. Our main contribution consists in using transfer learning in the encoder part of the UNet network, as well as test time augmentation when segmenting. We use the SE-Resnet50 backbone weights which was pre-trained on the ImageNet 2012 dataset. We used a data set of 23 images with the corresponding segmented masks, which also was challenging due to its extremely small size. The results show very encouraging performances compared to the state-of-the-art with an average precision of 92% on the test images. It is also important to note that the available samples were taken from elderly mices in the corpus callosum. This represented an additional difficulty, compared to related works that had samples taken from the spinal cord or the optic nerve of healthy individuals, with better contours and less debri

Identification par analyse en paquets d'ondelettes de l'iris et tests de robustesse

Cet article présente un système de reconnaissance par l'iris, fondé sur l'analyse en paquets d'ondelettes orthogonales. Une mesure d'énergie permet de choisir les paquets qui extraient l'information discriminante sur la texture de l'iris. Les tests, conduits sur une base de 149 images de très bonne qualité, provenant de 69 yeux différents, montrent une bonne robustesse aux conditions de prises de vues, notamment aux variations d'éclairement, au flou, à une déviation de l'axe optique, et à des défauts locaux dans l'image

Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo

Mammalian embryogenesis is a dynamic process involving gene expression and mechanical forces between proliferating cells. The exact nature of these interactions, which determine the lineage patterning of the trophectoderm and endoderm tissues occurring in a highly regulated manner at precise periods during the embryonic development, is an area of debate. We have developed a computational modeling framework for studying this process, by which the combined effects of mechanical and genetic interactions are analyzed within the context of proliferating cells. At a purely mechanical level, we demonstrate that the perpendicular alignment of the animal-vegetal (a-v) and embryonic-abembryonic (eb-ab) axes is a result of minimizing the total elastic conformational energy of the entire collection of cells, which are constrained by the zona pellucida. The coupling of gene expression with the mechanics of cell movement is important for formation of both the trophectoderm and the endoderm. In studying the formation of the trophectoderm, we contrast and compare quantitatively two hypotheses: (1) The position determines gene expression, and (2) the gene expression determines the position. Our model, which couples gene expression with mechanics, suggests that differential adhesion between different cell types is a critical determinant in the robust endoderm formation. In addition to differential adhesion, two different testable hypotheses emerge when considering endoderm formation: (1) A directional force acts on certain cells and moves them into forming the endoderm layer, which separates the blastocoel and the cells of the inner cell mass (ICM). In this case the blastocoel simply acts as a static boundary. (2) The blastocoel dynamically applies pressure upon the cells in contact with it, such that cell segregation in the presence of differential adhesion leads to the endoderm formation. To our knowledge, this is the first attempt to combine cell-based spatial mechanical simulations with genetic networks to explain mammalian embryogenesis. Such a framework provides the means to test hypotheses in a controlled in silico environment

Pydna: a simulation and documentation tool for DNA assembly strategies using python

Background: Recent advances in synthetic biology have provided tools to efficiently construct complex DNA molecules which are an important part of many molecular biology and biotechnology projects. The planning of such constructs has traditionally been done manually using a DNA sequence editor which becomes error-prone as scale and complexity of the construction increase. A human-readable formal description of cloning and assembly strategies, which also allows for automatic computer simulation and verification, would therefore be a valuable tool.Results: We have developed pydna, an extensible, free and open source Python library for simulating basic molecular biology DNA unit operations such as restriction digestion, ligation, PCR, primer design, Gibson assembly and homologous recombination. A cloning strategy expressed as a pydna script provides a description that is complete, unambiguous and stable. Execution of the script automatically yields the sequence of the final molecule(s) and that of any intermediate constructs. Pydna has been designed to be understandable for biologists with limited programming skills by providing interfaces that are semantically similar to the description of molecular biology unit operations found in literature.Conclusions: Pydna simplifies both the planning and sharing of cloning strategies and is especially useful for complex or combinatorial DNA molecule construction. An important difference compared to existing tools with similar goals is the use of Python instead of a specifically constructed language, providing a simulation environment that is more flexible and extensible by the user.Thanks to Dr. Aric Hagberg Los Alamos National Laboratory, U.S.A and Sergio Simoes, Universidade de Sao Paulo, Brasil for help with NetworkX and graph theory in general. Thanks to Henrik Bengtsson, Dept of Epidemiology & Biostatistics, University of California San Francisco, U.S.A. for critical reading of the manuscript. Thanks to the 2013 Bioinformatics 6605 N4 students A. Coelho, A. Faria, A. Neves D. Yelshyna and E. Costa for testing. This work was supported by the Fundacao para a Ciencia e Tecnologia (FCT) [PTDC/AAC-AMB/120940/2010, EXPL/BBB-BIO/1772/2013]; and the FEDER POFC-COMPETE [PEst-C/BIA/UI4050/2011]. FA and GR were supported by FCT fellowships [SFRH/BD/80934/2011 and SFRH/BD/42565/2007, respectively].info:eu-repo/semantics/publishedVersio

Characterization of visual object representations in rat primary visual cortex

For most animal species, quick and reliable identification of visual objects is critical for survival. This applies also to rodents, which, in recent years, have become increasingly popular models of visual functions. For this reason in this work we analyzed how various properties of visual objects are represented in rat primary visual cortex (V1). The analysis has been carried out through supervised (classification) and unsupervised (clustering) learning methods. We assessed quantitatively the discrimination capabilities of V1 neurons by demonstrating how photometric properties (luminosity and object position in the scene) can be derived directly from the neuronal responses

Global Chromatin Architecture Reflects Pluripotency and Lineage Commitment in the Early Mouse Embryo

An open chromatin architecture devoid of compact chromatin is thought to be associated with pluripotency in embryonic stem cells. Establishing this distinct epigenetic state may also be required for somatic cell reprogramming. However, there has been little direct examination of global structural domains of chromatin during the founding and loss of pluripotency that occurs in preimplantation mouse development. Here, we used electron spectroscopic imaging to examine large-scale chromatin structural changes during the transition from one-cell to early postimplantation stage embryos. In one-cell embryos chromatin was extensively dispersed with no noticeable accumulation at the nuclear envelope. Major changes were observed from one-cell to two-cell stage embryos, where chromatin became confined to discrete blocks of compaction and with an increased concentration at the nuclear envelope. In eight-cell embryos and pluripotent epiblast cells, chromatin was primarily distributed as an extended meshwork of uncompacted fibres and was indistinguishable from chromatin organization in embryonic stem cells. In contrast, lineage-committed trophectoderm and primitive endoderm cells, and the stem cell lines derived from these tissues, displayed higher levels of chromatin compaction, suggesting an association between developmental potential and chromatin organisation. We examined this association in vivo and found that deletion of Oct4, a factor required for pluripotency, caused the formation of large blocks of compact chromatin in putative epiblast cells. Together, these studies show that an open chromatin architecture is established in the embryonic lineages during development and is sufficient to distinguish pluripotent cells from tissue-restricted progenitor cells