Optimizing Voronoi-based quantifications for reaching interactive analysis of 3D localizations in the million range

Over the last decade, single-molecule localization microscopy (SMLM) has revolutionized cell biology, making it possible to monitor molecular organization and dynamics with spatial resolution of a few nanometers. Despite being a relatively recent field, SMLM has witnessed the development of dozens of analysis methods for problems as diverse as segmentation, clustering, tracking or colocalization. Among those, Voronoi-based methods have achieved a prominent position for 2D analysis as robust and efficient implementations were available for generating 2D Voronoi diagrams. Unfortunately, this was not the case for 3D Voronoi diagrams, and existing methods were therefore extremely time-consuming. In this work, we present a new hybrid CPU-GPU algorithm for the rapid generation of 3D Voronoi diagrams. Voro3D allows creating Voronoi diagrams of datasets composed of millions of localizations in minutes, making any Voronoi-based analysis method such as SR-Tesseler accessible to life scientists wanting to quantify 3D datasets. In addition, we also improve ClusterVisu, a Voronoi-based clustering method using Monte-Carlo simulations, by demonstrating that those costly simulations can be correctly approximated by a customized gamma probability distribution function

Triangulation of uniform particle systems: its application to the implicit surface texturing

Particle systems, as originally presented by Witkin and Heckbert [32], offer an elegant solution to sample implicit surfaces of arbitrary genus, while providing an extremely regular distribution of samples over the surface. In this paper, we present an ef cient technique that uses particle systems to rapidly generate a triangular mesh over an implicit surface, where each triangle is almost equilateral. The major advantage of such a triangulation is that it minimizes the deformations between the mesh and the underlying implicit surface. We exploit this property by using few triangular texture samples mapped in a non-periodic fashion as presented by Neyret and Cani [16]. The result is a pattern-based texturing method that maps homogeneous non-periodic textures to arbitrary implicit surfaces, with almost no deformation

Jeux vidéo et patrimoine : retour d’expérience sur le jeu Toulouse et le Petit Méridional de la Bûche Magique

Toulouse et le Petit Méridional est un jeu vidéo d’aventure et de réflexion s’attachant à valoriser le patrimoine de la presse ancienne numérisée, à travers le numéro du Petit Méridional du 30 mars 1909. Développé 110 ans plus tard par l’équipe de la Bûche Magique, soutenue et encadrée par la Région Occitanie, la filière Jeux vidéo de l’Université Paul Valéry Montpellier 3 et des acteurs locaux du milieu professionnel vidéoludique - Yoan Fanise, fondateur du studio DigixArt, Aline Krebs et Benjamin Dimanche, fondateurs du studio Homecoming - le jeu explore et expérimente des procédés de rencontre entre les spécificités du jeu vidéo et celles de la valorisation du patrimoine. Entre jeu expressif, rhétorique, artgame et gamification, Toulouse et le Petit Méridional permet de comprendre les tensions sous-jacentes à la création d’un jeu vidéo dans ses relations entre société, histoire et patrimoine.Toulouse et le petit Méridional is a video game of adventure and reflection that seeks to promote the heritage of the digitized ancient press, through the issue of Le Petit Méridional of March 30, 1909. Developed 110 years later by the Bûche Magique team, supported and supervised by the Occitanie Region, the video game department of the Paul Valéry University and local actors from the professional video game world - Yoan Fanise, founder of the Digixart studio, Aline Krebs and Benjamin Dimanche, founders of the Homecoming studio - the game explores and experiments with ways of bringing together the specificities of video games and those of heritage enhancement. From expressive game, rhetoric, artgame and gamification, Toulouse et le Petit Méridional allow us to understand the implicit tensions of the video game creation in its interaction between society, history and heritage

Multi-View Sketch-based FreeForm Modeling

International audienceFor the generation of freeform 3D models, one of the most intuitive solution is to use sketch-based modeling environments. Unfortunately, since the user interface relies upon the analyze of sketches in order to determine which action is requested by the user, the possible amount of different operations can be limited. In this paper, we present a 3D sketching system based on multiple views. Each view is specialized on a component of the modeling process (like the skeleton, the profile, etc.), and is based on specific sketching interactions. With this approach, an user could improve its understanding of the modeling process and per- form a larger range of modeling operations. Key words: Sketch-based 3D Modelin

Quantifying protein densities on cell membranes using super-resolution optical fluctuation imaging

Surface molecules, distributed in diverse patterns and clusters on cell membranes, influence vital functions of living cells. It is therefore important to understand their molecular surface organisation under different physiological and pathological conditions. Here, we present a model-free, quantitative method to determine the distribution of cell surface molecules based on TIRF illumination and super-resolution optical fluctuation imaging (SOFI). This SOFI-based approach is robust towards single emitter multiple-blinking events, high labelling densities and high blinking rates. In SOFI, the molecular density is not based on counting events, but results as an intrinsic property due to the correlation of the intensity fluctuations. The effectiveness and robustness of the method was validated using simulated data, as well as experimental data investigating the impact of palmitoylation on CD4 protein nanoscale distribution in the plasma membrane of resting T cells.Comment: 9 pages, 3 figures plus Supplementary Informatio

Echantillonnage anisotropique et rendu par points différentiels pour les surfaces implicites

Dans cet article, nous proposons une solution adaptant aux surfaces implicites, le rendu par points différentiels ("differential point rendering") de Kalaiah et Varshney [KV01] originellement développé pour les surfaces paramétriques et les maillages triangulaires. La principale difficulté pour cette adaptation est que les deux étapes du processus d'échantillonnage proposé dans [KV01] s'appuient fortement sur des relations de voisinage entre les échantillons, voisinage qui n'existe pas naturellement pour les surfaces implicites. Pour résoudre ce problème, nous proposons d'étudier les possibilités d'extensions de la technique d'échantillonnage par particules de Witkin et Heckbert [WH94] afin de prendre en compte les directions et les valeurs des courbures principales de la surface implicite. Ainsi, nous présenterons des résultats provenant d'une utilisation de particules ellipsoïdales ainsi que les problèmes inhérents à la nature même de l'ellipsoïde. Puis nous proposerons de nouvelles directions de recherche dans le but de résoudre ces problèmes

A tessellation-based colocalization analysis approach for single-molecule localization microscopy

International audienceMulticolor single-molecule localization microscopy (λSMLM) is a powerful technique to reveal the relative nanoscale organization and potential colocalization between different molecular species. While several standard analysis methods exist for pixel-based images, λSMLM still lacks such a standard. Moreover, existing methods only work on 2D data and are usually sensitive to the relative molecular organization, a very important parameter to consider in quantitative SMLM. Here, we present an efficient, parameter-free colocalization analysis method for 2D and 3D λSMLM using tessellation analysis. We demonstrate that our method allows for the efficient computation of several popular colocalization estimators directly from molecular coordinates and illustrate its capability to analyze multicolor SMLM data in a robust and efficient manner

Multi-synaptic boutons are a feature of CA1 hippocampal connections in the stratum oriens

Excitatory synapses are typically described as single synaptic boutons (SSBs), where one presynaptic bouton contacts a single postsynaptic spine. Using serial section block-face scanning electron microscopy, we found that this textbook definition of the synapse does not fully apply to the CA1 region of the hippocampus. Roughly half of all excitatory synapses in the stratum oriens involved multi-synaptic boutons (MSBs), where a single presynaptic bouton containing multiple active zones contacted many postsynaptic spines (from 2 to 7) on the basal dendrites of different cells. The fraction of MSBs increased during development (from postnatal day 22 [P22] to P100) and decreased with distance from the soma. Curiously, synaptic properties such as active zone (AZ) or postsynaptic density (PSD) size exhibited less within-MSB variation when compared with neighboring SSBs, features that were confirmed by super-resolution light microscopy. Computer simulations suggest that these properties favor synchronous activity in CA1 networks

EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats

International audienceThe ontology of bioimage informatics operations, topics, data, and formats What? EDAM-bioimaging is an extension of the EDAM ontology, dedicated to bioimage analysis, bioimage informatics, and bioimaging. Why? EDAM-bioimaging enables interoperable descriptions of software, publications, data, and workflows, fostering reliable and transparent science. How? EDAM-bioimaging is developed in a community spirit, in a welcoming collaboration between numerous bioimaging experts and ontology developers. How can I contribute? We need your expertise! You can help by reviewing parts of EDAM-bioimaging, posting comments with suggestions, requirements, or needs for clarification, or participating in a Taggathon or another hackathon. Please see https://github.com/edamontology/edam-bioimaging#contributing. EDAM-bioimaging is developed in an interdisciplinary open collaboration supported by the hosting institutions, participating individuals, and NEUBIAS COST Action (CA15124) and ELIXIR-EXCELERATE (676559) funded by the Horizon 2020 Framework Programme of the European Union. https://github.com/edamontology/edam-bioimaging @edamontology /edamontology/edam-bioimagin

flevet/PoCA: 0.10.0

<p>Corrected a few bugs (crops in 3D could cause PoCA to crash because of an OpenGL instability, Python pre-defined modules were not working, etc.) and added a couple of stuffs like tool tips with histograms. Added a crop of microtubulles in 3D in the data folder.</p&gt