Marker-free image registration of electron tomography tilt-series

<p>Abstract</p> <p>Background</p> <p>Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3D reconstruction. Current alignment techniques usually employ gold particles or image derived markers to correctly align the images. When these markers are not present, correlation between adjacent views is used to align them. However, sequential pairwise correlation is prone to bias and the resulting alignment is not always optimal.</p> <p>Results</p> <p>In this paper we introduce an algorithm to find regions of the tilt series which can be tracked within a subseries of the tilt series. These regions act as landmarks allowing the determination of the alignment parameters. We show our results with synthetic data as well as experimental cryo electron tomography.</p> <p>Conclusion</p> <p>Our algorithm is able to correctly align a single-tilt tomographic series without the help of fiducial markers thanks to the detection of thousands of small image patches that can be tracked over a short number of images in the series.</p

Parlons peu, parlons chercheur au quotidien... sur son terrain

Si nous travaillons tous les trois sur des objets différents et appartenons parfois à des disciplines différentes, nous avons la même appétence pour les questions qui touchent de près, ou de loin, à l’impact de notre propre façon de concevoir nos objets d’étude ainsi que sur la manière de produire nos données et de concevoir notre méthodologie. L’atelier d’écriture a servi de point de départ à cette réflexion et, après quelques passionnantes discussions qui auraient pu durer des heures, nous avons constaté que consacrer un temps spécifique à ces questions – en les démêlant et en cherchant à davantage les problématiser – pouvait être pertinent. Sachant que d’autres collègues sont tout aussi animé·e·s que nous par ce genre de questions rarement mises sur la table, nous avons opté dans un premier temps pour une mise en place d'au moins deux midis sur la question. Nous pourrons ainsi partager le fruit de nos réflexions en cours, et en retour, profiter de l’expérience et des conceptions de chacun·e. Il s’agira d’entrer dans les coulisses de nos recherches respectives avec honnêteté, rigueur et humilité. Il s’agira avant tout de poser des réflexions partant de situations concrètement vécues qui ont pu induire d’éventuels malaises ou doutes par rapport à sa propre posture voire, de façon plus fondamentale, sur son rôle en tant que chercheur ou chercheuse. Si cette dernière question est souvent laissée à l’appréciation de chacun·e nous souhaiterions la sortir de l’ombre pour offrir la possibilité à tout le monde de bénéficier de l’expérience concrète des autres et de mettre à l’épreuve ses propres pratiques. Voici une série de questions qui guideront nos échanges : si, pour comprendre les pratiques de tel ou tel acteur social, est considérée comme tout à fait pertinente l’observation et la description in situ des relations en train de se faire, que faire des réactions des acteurs par rapport à notre présence sur leur terrain et comment – si c’est pertinent – les intégrer à la recherche ? Si l’analyse des discours de certains acteurs à travers les textes qu’ils·elles produisent constitue le point nodal de la recherche, quelle place donner à un échange avec ces acteurs et comment l’intégrer à la recherche ? De manière générale, est-il nécessaire d’échanger avec les acteurs de notre terrain et, dans l’affirmative, comment intégrer ces échanges dans la recherche ? En résumé, lorgnette, ping-pong ou natation synchronisée : quel est VOTRE rapport au terrain

An ImageJ tool for simplified post-treatment of TEM phase contrast images (SPCI)

International audienceTools for taking advantage of phase-contrast in transmission electron microscopy are of great interest for both biological and material sciences studies as shown by the recent use of phase plates and the development of holography. Nevertheless, these tools most often require highly qualified experts and access to advanced equipment that can only be considered after preliminary investigations. Here we propose to address this issue by the development of an ImageJ plugin that allow the retrieval of a phase image by simple numerical treatment applied to two defocused images. This treatment based on Tikhonov regularization requires the adjustment of a single parameter. Moreover, it is possible to use this approach on one-image. Although in that case the retrieved image gives only qualitative information, it is able to enhance the image contrast appropriately. This can be of interest for specimens producing low contrast images under the electron microscopes, such as some frozen hydrated biological samples or those sensible to electron radiation unsuitable for holographic studies

Scanning transmission electron microscopy through-focal tilt-series on biological specimens

International audienceSince scanning transmission electron microscopy can produce high signal-to-noise ratio bright-field images of thick (>= 500 nm) specimens, this tool is emerging as the method of choice to study thick biological samples via tomographic approaches. However, in a convergent-beam configuration, the depth of field is limited because only a thin portion of the specimen (from a few nanometres to tens of nanometres depending on the convergence angle) can be imaged in focus. A method known as through-focal imaging enables recovery of the full depth of information by combining images acquired at different levels of focus. In this work, we compare tomographic reconstruction with the through-focal tilt-series approach (a multifocal series of images per tilt angle) with reconstruction with the classic tilt-series acquisition scheme (one single-focus image per tilt angle). We visualised the base of the flagellum in the protist Trypanosoma brucei via an acquisition and image-processing method tailored to obtain quantitative and qualitative descriptors of reconstruction volumes. Reconstructions using through-focal imaging contained more contrast and more details for thick (>= 500 nm) biological samples. (C) 2015 Elsevier Ltd. All rights reserved

Determination of Microtubule Lattice Parameters from Cryo-electron Microscope Images Using TubuleJ

International audienceThe α-β tubulin heterodimer undergoes subtle conformational changes during microtubule assembly. These can be modulated by external factors, whose effects on microtubule structure can be characterized on 2D views obtained by cryo-electron microscopy. Analysis of microtubule images is facilitated if they are straight enough to interpret and filter their image Fourier transform, which provide useful information concerning the arrangement of tubulin molecules inside the microtubule lattice. Here, we describe the use of the TubuleJ software to straighten microtubules and determine their lattice parameters. Basic 3D reconstructions can be performed to evaluate the relevance of these parameters. This approach can be used to analyze the effects of nucleotide analogues, drugs or MAPs on microtubule structure, or to select microtubule images prior to high-resolution 3D reconstructions

Diamond Inter-Digited JFET for Power Electronic Devices

International audienc

Diamond Inter-Digited JFET for Power Electronic Devices

International audienc

The Lactobacillus plantarum strain ACA-DC287 isolated from a Greek cheese demonstrates antagonistic activity in vitro and in vivo against Salmonella enterica serovar Typhimurium.

International audienceAIMS: The purpose of this study was to investigate the antibacterial activity of the Xynotyri cheese isolate Lactobacillus plantarum ACA-DC287 using a set of in vitro and in vivo assays. METHODS AND RESULTS: The co-culture of L. plantarum strain ACA-DC287 and Salmonella enterica serovar Typhimurium strain SL1344 results in the killing of the pathogen. The killing activity was produced mainly by non-lactic acid molecule(s) that were present in the cell-free culture supernatant of the L. plantarum strain ACA-DC287. The culture of the L. plantarum strain ACA-DC287 inhibited the penetration of S. typhimurium SL1344 into cultured human enterocyte-like Caco-2/TC7 cells. In conventional mice infected with S. typhimurium SL1344, the intake of L. plantarum strain ACA-DC287 results in a decrease in the levels of Salmonella associated with intestinal tissues or those present in the intestinal contents. In germ-free mice, the L. plantarum strain ACA-DC287 colonized the gastrointestinal tract. CONCLUSIONS: The L. plantarum strain ACA-DC287 strain exerts anti-Salmonella activity similar that of the established probiotic strains Lactobacillus rhamnosus GG, Lactobacillus casei Shirota YIT9029 and Lactobacillus johnsonii La1. SIGNIFICANCE AND IMPACT OF THE STUDY: The observation that a selected cheese Lactobacillus strain exerted antibacterial activity that was similar to those of probiotic Lactobacillus strains, is of interest for the use of this strain as an adjunct strain for the production of health-giving cheeses