Alexandre Dufour

TotalEnergies · Imaging Centre of Excellence

Variational deformable models have proven over the past decades a high efficiency for segmentation and tracking in 2-D sequences. Yet, their application to 3-D time-lapse images has been hampered by discretization issues, heavy computational loads and lack of proper user visualization and interaction, limiting their use for routine analysis of larg...

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 workflow...

Cell motility is governed by a complex molecular machinery that converts physico-chemical cues into whole-cell movement. Understanding the underlying biophysical mechanisms requires the ability to measure physical quantities inside the cell in a simple, reproducible and preferably non-invasive manner. To this end, we developed BioFlow, a computatio...

In this paper, we propose a new experimental set-up to carry out a full Amott-like cycle on small core samples (4 mm. diameter, 15 mm. length), imaged with a high-resolution micro-CT scanner. We conduct this experiment on two core samples from a carbonate reservoir. Each step of the cycle was followed by a 3D highresolution scan along the entire sa...

Collective transmission via structures containing several virions has recently emerged as a highly efficient mode of viral spread. Here, we demonstrate that HIV-1 spreads between T lymphocytes in the form of viral particles colonies that are concentrated and sheltered in an extracellular matrix (ECM) lattice enabling their collective transmission u...

Establishment of a fungal infection due to Aspergillus fumigatus relies on the efficient germination of the airborne conidia once they penetrate the respiratory tract. However, the features of conidial germination have been poorly explored and understood in this fungal species as well as in other species of filamentous fungi. We show here that the...

Accurate measurements of cell morphology and behaviour are fundamentally important for understanding how disease, molecules and drugs affect cell function in vivo . Here, by using muscle stem cell (muSC) responses to injury in zebrafish as our biological paradigm, we established a ‘ground truth’ for muSC behaviour. This revealed that segmentation a...

Accurate measurements of cell morphology and behaviour are fundamentally important for understanding how disease, molecules and drugs affect cell function in vivo. Using muscle stem cell (muSC) responses to injury in zebrafish as our biological paradigm we have established a ground truth for muSC cell behaviour. This revealed that variability in se...

To invade cells, the parasite Toxoplasma gondii injects a multi-unit nanodevice into the target cell plasma membrane (PM). The core nanodevice, which is composed of the RhOptry Neck (RON) protein complex, connects Toxoplasma and host cell through a circular tight junction (TJ). We now report that this RON nanodevice mechanically promotes membrane s...

Elucidating protein functions and molecular organisation requires to localise precisely single or aggregated molecules and analyse their spatial distributions. We develop a statistical method SODA (Statistical Object Distance Analysis) that uses either micro- or nanoscopy to significantly improve on standard co-localisation techniques. Our method c...

EDAM is a well-established ontology of operations, topics, types of data, and data formats that are used in bioinformatics and its neighbouring fields [1,2,3]. EDAM-bioimaging is an extension of EDAM dedicated to bioimage analysis, bioimage informatics, and bioimaging. It is developed in collaboration between the NEUBIAS and ELIXIR Europe|ELIXIR-EX...

Salmonella targets and enters epithelial cells at permissive entry sites: some cells are more likely to be infected than others. However, the parameters that lead to host cell heterogeneity are not known. Here, we quantitatively characterized host cell “vulnerability” towards Salmonella infection based on imaged parameters. We performed successive...

We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challe...

Inner cell Mass (ICM) specification into epiblast (Epi) and primitive endoderm (PrE) is an asynchronous and progressive process taking place between E3.0 to E3.75 under the control of the Fibroblast Growth Factor (FGF)/Extracellular signal-Regulated Kinase (ERK) signaling pathway. Here, we have analyzed in details the kinetics of specification and...

Inner cell Mass (ICM) specification into epiblast (Epi) and primitive endoderm (PrE) is an asynchronous and progressive process taking place between E3.0 to E3.75 under the control of the FGF/ERK signaling pathway. Here, we have analyzed in details the kinetics of specification and found that ICM cell responsiveness to the up and down regulation of...

Salmonella target and enter epithelial cells at permissive entry sites: some cells are more likely to be infected than others. However the parameters that lead to host cell heterogeneity are not known. Here, we quantitatively characterized host cell ‘vulnerability’ towards Salmonella infection based on imaged parameters. We performed successive inf...

Although in flies the atypical cadherin Fat is an upstream regulator of Hippo signalling, the closest mammalian homologue, Fat4, has been shown to regulate tissue polarity rather than growth. Here we show in the mouse heart that Fat4 modulates Hippo signalling to restrict growth. Fat4 mutant myocardium is thicker, with increased cardiomyocyte size...

In recent years developmental biology has greatly benefited from the latest advances in fluorescence microscopy techniques. Consequently, quantitative and automated analysis of this data is becoming a vital first step in the quest for novel insights into the various aspects of development. Here we present an introductory overview of the various ima...

Tissue mimics (TMs) on the scale of several hundred microns provide a beneficial cell culture configuration for in vitro engineered tissue and are currently under the spotlight in tissue engineering and regenerative medicine. Due to the cell density and size, TMs are fairly inaccessible to optical observation and imaging within these samples remain...

Supplementary figures and supplementary tables.

Invasion and multiplication of the facultative, cytosolic, enteropathogen Shigella flexneri within the colonic epithelial lining leads to an acute inflammatory response, fever and diarrhea. During the inflammatory process, infected cells are subjected to numerous stresses including heat, oxidative stress and genotoxic stress. The evolutionarily con...

Human liver infection is a major cause of death worldwide, but fundamental studies on infectious diseases affecting humans have been hampered by the lack of robust experimental models that accurately reproduce pathogen-host interactions in an environment relevant for the human disease. In the case of liver infection, one consequence of this absence...

Supporting Information. Method details on the HBV production and infection, RT-qPCR) to measure HBV transcripts, two-photon microscopy and iron quantification in different fractions of the 3D liver model. (DOCX)

The development of amoebiasis disease is influenced by the expression of the lysine and glutamic acid rich protein 1 (KERP1), a virulence factor involved in Entamoeba histolytica adherence to human cells. Up to date, it is unknown how the protein transits the parasite cytoplasm towards the plasma membrane, especially since this organism lacks a wel...

Entamoeba histolytica, the causative agent of amoebiasis, is a protozoan parasite characterised by its amoeboid motility, which is essential to its survival and invasion of the human host. Elucidating the molecular mechanisms leading to invasion of human tissues by E. histolytica requires a quantitative understanding of how its cytoskeleton deforms...

Modern developments in light microscopy have allowed the observation of cell deformation with remarkable spatiotemporal resolution and reproducibility. Analyzing such phenomena is of particular interest for the signal processing and computer vision communities due to the numerous computational challenges involved, from image acquisition all the way...

Chlamydiae are obligate intracellular bacteria. These pathogens develop inside host cells through a biphasic cycle alternating between two morphologically distinct forms, the infectious elementary body and the replicative reticulate body. Recently, C. trachomatis strains stably expressing fluorescent proteins were obtained. The fluorochromes are ex...

Amoeboid cell motility is characterised by the emission of protrusions at the cellular surface (also known as “blebs”). Detection and counting of these protrusions is a crucial step towards the understanding of the deformation and motility machinery. We propose an automated technique to detect protrusions at the surface of cells observed in 3D fluo...

We propose a realistic model of cell and membrane deformations based on fluid mechanics. We focus on the blebbing process, a key mechanism of motility for several cell types. It is seen as a rupture of symmetry in the surface tension forces affecting the membrane of the cell. It produces sudden protrusions in regions where the tension forces vanish...

The deformation process orchestrated by the cell machinery is particularly complex and characterized by shape changes at multiple geometrical scales to drive cell deformation and movement. Precise cell shape description tools have become necessary to detect shape changes in a robust manner to allow subsequent morpho-dynamic profiling. Here we inves...

Listeria monocytogenes (Lm) is a ubiquitous bacterium able to survive and thrive within the environment and readily colonizes a wide range of substrates, often as a biofilm. It is also a facultative intracellular pathogen, which actively invades diverse hosts and induces listeriosis. So far, these two complementary facets of Lm biology have been st...

ActA promotes clinical isolates and EGDe aggregation within gut lumen and favors intestinal colonization. (A) Imaging of EGDe ΔactA + actA (EGDe ActA+) and EGDe ΔactA + actAΔC (EGDe ΔC+) mutants within stools of 96 h-infected mice. Lm was labeled with anti-Lm (red) and nuclei with Hoechst (blue). Scale: 2 µm. (B) Colonization assay performed on eig...

Strains used in this study. All the strains used in the study are listed and referenced. Plasmids used for mutant complementation are cited and also references. Origin of the complementation genes, as well as the promoter and the ribosome-binding site allowing their expression, are noted. CmR: chloramphenicol-resistant. (DOC)

Primers used in this study. Primers used for construction of EGD ΔprfA (prfA-1-F, prfA-1-R, prfA-2-F and prfA-2-R), EGD ΔprfA + prfA (prfA-5 and prfA-3), EGDe ΔactA (actA-L1, actA-R1, actA-L2 and actA-R2), EGD ΔactA + actA (actA-5-F and actA-200-3-R) and EGD ΔactA + actAΔC (actA-5-F, actA-AA441-3, actA-AA608-5 and actA-200-3-R) are listed. (DOC)

actA, a PrfA-regulated gene, mediates LO28 and EGDe aggregation. (A) Results of aggregation assays performed on LO28 WT strain and LO28 Tn::prfA in BHI. (B) Results of aggregation assays performed on EGDe WT strain and EGDe ΔprfA in BHI. (C) Results of aggregation assays performed on LO28 WT strain and LO28 Tn::prfA in DMEM to increase PrfA-regulat...

ActA expression analysis. (A) Immunoblot performed on NRC strains including the PrfA+ isolates and the PrfA− isolates. ActA was revealed using the anti-ActA P473 antibody and the amount of loaded bacteria was controlled using the anti-EF-Tu R-114. (B) Immunoblot performed on LO28 truncated mutants of ActA. ActA was revealed using the anti-ActA A18K...

Motivation: In developmental biology, quantitative tools to extract features from fluorescence microscopy images are becoming essential to characterize organ morphogenesis at the cellular level. However, automated image analysis in this context is a challenging task, owing to perturbations induced by the acquisition process, especially in organism...

Anisotropies that underlie organ morphogenesis have been quantified in 2D, taking advantage of a reference axis. However, morphogenesis is a 3D process and it remains a challenge to analyze cell polarities in 3D. Here, we have designed a novel procedure that integrates multidisciplinary tools, including image segmentation, statistical analyses, axi...

Bioimage informatics has emerged as a new interdisciplinary research endeavor for bringing the power of computational and mathematical sciences into the biological imaging arena. We describe an open-source software platform, Icy, that proposes a comprehensive framework for easy algorithm development and deployment fostering community-oriented effor...

We aim at analysing fluorescence microscopy sequences of moving cells, so as to estimate the velocities that define the movement, the forces that drive this movement, and the pressure that characterises the material state. We use an optical flow method constrained by Stokes flow mechanics equations that define the dynamics of a fluid that is incomp...

Understanding the mechanisms involved in cell deformation and motility is of major interest in numerous areas of life sciences. Precise quantification of cell shape requires robust shape description tools to be amenable to subsequent analysis and classification. The main difficulty lies in the great variability of cell shapes within so-called ”homo...

The extracellular matrix (ECM) and its role in the outcome of infectious diseases have been poorly investigated. In this study, we determined the impact of the collagen fibres architecture on the invasive process of the enteric parasite Entamoeba histolytica. The behaviour of E. histolytica wild-type and silenced for the cysteine protease A5 (CP-A5...

Image filtering methods are crucial in a large number of applications where the relevant information is either noisy or partially missing. More particularly in 3D microscopy, cell membranes appear as structures of co-dimension 2, and suffer from discontinuities in intensity and orientation. Anisotropic PDE-based approaches offer an elegant solution...

Understanding the mechanisms involved in cell deformation and motility is of major interest in numerous areas of life sciences. Precise quantification of cell shape requires robust shape description tools to be amenable to subsequent analysis and classification. The main difficulty lies in the great variability of cell shapes within a given homogen...

Confocal fluorescence microscopy has become a standard tool to image thick 3D tissue samples, permitting the observation of cell behaviour, such as cell division within developing organs. However, robust and automatic extraction of nuclear shape and mitotic orientation may be hindered by a highly cluttered environment as for example in mammalian ti...

CFSE-stained aNK cells induce apoptosis of immature DCs in aNK-DC cocultures but do not die. (A) CD56+ NK cells sorted from PBMC were activated with PHA+IL-2 (aNK) and cultured for 24 h either alone or in the presence of iDCs generated from purified CD14+ monocytes in the presence of IL-4 and GM-CSF (NK∶DC ratio 5∶1). The survival of CD3negCD56+ ce...

Early stages of Human Immunodeficiency Virus-1 (HIV-1) infection are associated with local recruitment and activation of important effectors of innate immunity, i.e. natural killer (NK) cells and dendritic cells (DCs). Immature DCs (iDCs) capture HIV-1 through specific receptors and can disseminate the infection to lymphoid tissues following their...

Growing evidence indicates that kinases are central to the regulation of endocytic pathways. Previously, we identified p21-activated kinase 1 (Pak1) as the first specific regulator of clathrin- and caveolae-independent endocytosis used by the interleukin 2 receptor subunit (IL-2R). Here, we address the mechanism by which Pak1 regulates IL-2Rbeta en...

This paper presents a novel approach to track multiple articulated objects in a video sequence. The key idea is to define a model of the object using a set of geometrical primitives linked by physical constraints, and exploit physics engines to solve these constraints while the model adapts to the object under the influence of local mean-shift proc...

Recent advances in fluorescence microscopy provide us with an unprecedented powerful way to observe many biological objects (pathogens, vesicles, single molecules, etc.) and events (intracellular trafficking, adhesion, migration, pathogens entry) in the living cell under multiple experimental conditions. To understand the underlying biological phen...

This paper tackles the problem of tracking multiple articulated objects undergoing frequent contacts in a video sequence. Conventional tracking methods usually fail to distinguish objects during contact, implying the use of disambiguation techniques to recover the identity of each object. Moreover, such methods do not provide detailed shape informa...

Understanding subcellular dynamic processes governing pathogenic mechanisms is a necessary step towards the development of new drugs and strategies against infectious diseases. Subcellular pathogenic mechanisms, such as viral invasion processes involve highly dynamic nanometric-scale objects and rapid molecular interactions that require the study o...