Nicolas Chenouard

Icy: an open bioimage informatics platform for extended reproducible research

Current research in biology uses evermore complex computational and imaging tools. Here we describe Icy, a collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless development of sophisticated imaging workflows. Icy extends the reproducible research principles, by encouraging and facilitating the reusability, modularity, standardization and management of algorithms and protocols. Icy is free, open-source and available at http://icy.bioimageanalysis.org/.

Prions hijack tunnelling nanotubes for intercellular spread

In variant Creutzfeldt–Jakob disease, prions (PrPSc) enter the body with contaminated foodstuffs and can spread from the intestinal entry site to the central nervous system (CNS) by intercellular transfer from the lymphoid system to the peripheral nervous system (PNS). Although several means and different cell types have been proposed to have a role, the mechanism of cell-to-cell spreading remains elusive. Tunnelling nanotubes (TNTs) have been identified between cells, both in vitro and in vivo, and may represent a conserved means of cell-to-cell communication. Here we show that TNTs allow transfer of exogenous and endogenous PrPSc between infected and naive neuronal CAD cells. Significantly, transfer of endogenous PrPSc aggregates was detected exclusively when cells chronically infected with the 139A mouse prion strain were connected to mouse CAD cells by means of TNTs, identifying TNTs as an efficient route for PrPSc spreading in neuronal cells. In addition, we detected the transfer of labelled PrPSc from bone marrow-derived dendritic cells to primary neurons connected through TNTs. Because dendritic cells can interact with peripheral neurons in lymphoid organs, TNT-mediated intercellular transfer would allow neurons to transport prions retrogradely to the CNS. We therefore propose that TNTs are involved in the spreading of PrPSc within neurons in the CNS and from the peripheral site of entry to the PNS by neuroimmune interactions with dendritic cells.

Multiple Hypothesis Tracking for Cluttered Biological Image Sequences

In this paper, we present a method for simultaneously tracking thousands of targets in biological image sequences, which is of major importance in modern biology. The complexity and inherent randomness of the problem lead us to propose a unified probabilistic framework for tracking biological particles in microscope images. The framework includes realistic models of particle motion and existence and of fluorescence image features. For the track extraction process per se, the very cluttered conditions motivate the adoption of a multiframe approach that enforces tracking decision robustness to poor imaging conditions and to random target movements. We tackle the large-scale nature of the problem by adapting the multiple hypothesis tracking algorithm to the proposed framework, resulting in a method with a favorable tradeoff between the model complexity and the computational cost of the tracking procedure. When compared to the state-of-the-art tracking techniques for bioimaging, the proposed algorithm is shown to be the only method providing high-quality results despite the critically poor imaging conditions and the dense target presence. We thus demonstrate the benefits of advanced Bayesian tracking techniques for the accurate computational modeling of dynamical biological processes, which is promising for further developments in this domain.

Intraflagellar transport proteins cycle between the flagellum and its base

Summary Intraflagellar transport (IFT) is necessary for the construction of cilia and flagella. IFT proteins are concentrated at the base of the flagellum but little is known about the actual role of this pool of proteins. Here, IFT was investigated in Trypanosoma brucei, an attractive model for flagellum studies, using GFP fusions with IFT52 or the IFT dynein heavy chain DHC2.1. Tracking analysis by a curvelet method allowing automated separation of forward and return transport demonstrated a uniform speed for retrograde IFT (5 µm s−1) but two distinct populations for anterograde movement that are sensitive to temperature. When they reach the distal tip, anterograde trains are split into three and converted to retrograde trains. When a fast anterograde train catches up with a slow one, it is almost twice as likely to fuse with it rather than to overtake it, implying that these trains travel on a restricted set of microtubules. Using photobleaching experiments, we show for the first time that IFT proteins coming back from the flagellum are mixed with those present at the flagellum base and can reiterate a full IFT cycle in the flagellum. This recycling is dependent on flagellum length and IFT velocities. Mathematical modelling integrating all parameters actually reveals the existence of two pools of IFT proteins at the flagellum base, but only one is actively engaged in IFT.

A Unifying Parametric Framework for 2D Steerable Wavelet Transforms

We introduce a complete parameterization of the family of two-dimensional steerable wavelets that are polar-separable in the Fourier domain under the constraint of self-reversibility. These wavelets are constructed by multiorder generalized Riesz transformation of a primary isotropic bandpass pyramid. The backbone of the transform (pyramid) is characterized by a radial frequency profile function

Multiple hypothesis tracking in microscopy images

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In vivo colocalisation of oskar mRNA and trans-acting proteins revealed by quantitative imaging of the Drosophila oocyte.

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Tracking algorithms chase down pathogens.

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3D steerable wavelets and monogenic analysis for bioimaging

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A Dual Role for Actin and Microtubule Cytoskeleton in the Transport of Golgi Units from the Nurse Cells to the Oocyte Across Ring Canals

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