A5033642367- Cell Image Analysis Techniques
- Cellular Mechanics and Interactions
- Advanced Fluorescence Microscopy Techniques
- Single-cell and spatial transcriptomics
- Zebrafish Biomedical Research Applications
- Hippo pathway signaling and YAP/TAZ
- Developmental Biology and Gene Regulation
- Agricultural Innovations and Practices
- Medical Image Segmentation Techniques
- Marine animal studies overview
- Congenital heart defects research
- Muscle Physiology and Disorders
- Underwater Vehicles and Communication Systems
- Neurogenesis and neuroplasticity mechanisms
- Gene expression and cancer classification
- BRCA gene mutations in cancer
- Food Safety and Hygiene
- Impact of Light on Environment and Health
- Mathematical Biology Tumor Growth
- Agricultural Economics and Policy
- ICT in Developing Communities
- PARP inhibition in cancer therapy
- Gene Regulatory Network Analysis
- Receptor Mechanisms and Signaling
- Advanced Vision and Imaging
Queen Mary University of London
2025
Response Biomedical (Canada)
2024
Target (United States)
2024
Centre National de la Recherche Scientifique
2010-2023
Université Paris-Saclay
2016-2023
Laboratoire Matière et Systèmes Complexes
2010-2023
Université Paris Cité
2023
Laboratoire de Neurobiologie Cellulaire et Moléculaire
2014-2021
Biogéosciences
2021
Institute for Complex Systems
2019
Quantifying cell behaviors in animal early embryogenesis remains a challenging issue requiring toto imaging and automated image analysis. We designed framework for reconstructing unstained whole zebrafish embryos their first 10 division cycles report measurements along the lineage with micrometer spatial resolution minute temporal accuracy. Point-scanning multiphoton excitation optimized to preferentially probe innermost regions of embryo provided intrinsic signals highlighting all mitotic...
Resistance to therapies that target homologous recombination deficiency (HRD) in breast cancer limits their overall effectiveness. Multiple, preclinically validated, mechanisms of resistance have been proposed, but existence and relative frequency clinical disease are unclear, as is how resistance.
Toxicity is one of the major attrition causes during drug development process. In that line, cardio-, neuro-, and hepatotoxicities are among main reasons behind retirement drugs in clinical phases post market withdrawal. Zebrafish exploitation high-throughput screening becoming an important tool to assess toxicity efficacy novel drugs. This animal model has, from early developmental stages, fully functional organs a physiological point view. Thus, drug-induced organ-toxicity can be detected...
Abstract The quantitative and systematic analysis of embryonic cell dynamics from in vivo 3D+time image data sets is a major challenge at the forefront developmental biology. Despite recent breakthroughs microscopy imaging living systems, producing an accurate lineage tree for any developing organism remains difficult task. We present here BioEmergences workflow integrating all reconstruction steps acquisition processing to interactive visualization reconstructed data. Original mathematical...
During morphogenesis, embryonic tissues display fluid-like behavior with fluctuating strain rates. Digital cell lineages reconstructed from 4D images of developing zebrafish embryos are used to infer representative tissue deformation patterns and their association developmental events. Finite analysis along trajectories unsupervised machine learning applied obtain reduced-order models condensing the collective motions, delineating domains distinct biomechanical behavior. This kinematic...
Investigating neural stem cell (NSC) behaviour in vivo, which is a major area of research, requires NSC models to be developed. We carried out multilevel characterisation the zebrafish embryo peripheral midbrain layer (PML) and identified unique vertebrate progenitor population. Located dorsally transparent midbrain, these large slow-amplifying progenitors (SAPs) are accessible for long-term vivo imaging. They form neuroepithelial adjacent optic tectum, has transitory fast-amplifying (FAPs)...
A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time space. The automated reconstruction a prototypic 4D for vertebrate early embryos, using multicolor fluorescence situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed original methodological framework implemented software tool called Match-IT. With only minimal human supervision, our system able gather...
Reconstructing the lineage of cells is central to understanding how wide diversity cell types develops. Here, we provide neurosensory reconstruction a complex sensory organ, inner ear, by imaging zebrafish embryos in vivo over an extended timespan, combining tracing and fate marker expression time. We deliver first dynamic map early neuronal progenitor pools whole otic vesicle. It highlights remodeling domain upon neuroblast delamination, reveals that order place neuroblasts’ delamination...
Abstract We conducted a quantitative comparison of developing sea urchin embryos based on the analysis five digital specimens obtained by automatic processing in toto 3D+ time image data. These measurements served reconstruction prototypical cell lineage tree able to predict spatiotemporal cellular organisation normal blastula. The was achieved designing and tuning multi-level probabilistic model that reproduced embryo-level dynamics from small number statistical parameters characterising...
Abstract Tissue internalisation is a key morphogenetic mechanism by which embryonic tissues generate complex internal organs and number of studies epithelia have outlined general view tissue internalisation. Here we used quantitative live imaging mutant analysis to determine whether similar mechanisms are responsible for in that apparently does not typical epithelial organisation – the zebrafish neural plate. We found although embryos begin neurulation without conventional epithelium,...
We propose to directly process 3D + t image sequences with mathematical morphology operators using a new classification of the 3D+t structuring elements. Several methods (filtering, tracking, segmentation) dedicated analysis datasets zebrafish embryogenesis are introduced and validated through synthetic dataset. Then, we illustrate application these early development acquired various microscopy techniques. This processing paradigm produces spatio-temporal coherent results as it benefits from...
We test the hypothesis that cell membranes in early sea- urchin embryos can be modeled as a Voronoi diagram from nuclei centers. In order to obtain model of geometry against which our hypothesis, we developed viscous watershed framework allows segmenting 3D images living sea-urchin obtained by biphoton laser scanning microscopy. Measurements differences between segmented cells and model, show an interesting high correlation serve for developing more accurate methods segmentation modelling geometries.
We present a simple and parameter-free nuclei tracking method for reconstructing cell dynamics in fluorescence 3D+t images of embryogenesis. The strategy is based on the use mathematical morphology operators directly 4D image. morphological reconstruction marker -manually or automatically selected- an initial spatio-temporal position generates connected path over time representing migration. Thus, processing provides coherent spatiotemporal estimation movement. algorithm has been validated...
We elaborate on a general framework composed of set computational tools to accurately quantificate cellular position and gene expression levels throughout early zebrafish embryogenesis captured over time-lapse series in vivo 3D images. Our modeling strategy involves nuclei detection, cell geometries extraction, automatic quantification tracking reconstruct trajectories lineage tree which describe the animal development. Each embryo is then precisely described at each given time t by vector...
Abstract Digital cell lineages reconstructed from 3D+time imaging data provide unique information to unveil mechanical cues and their role in morphogenetic processes. Our methodology based on a kinematic analysis of lineage reveals deformation patterns quantitative landmarks for new type developmental table. The characteristic spatial temporal length scales derived continuous approximation displacements indicate compressible fluid-like behavior zebrafish gastrulating tissues. instantaneous...
Fires, lights at night and mobile phone activity have been separately used as proxy indicators of human with high potential for measuring development. In this preliminary report, we develop some tools methodologies to identify visualize relations among remote sensing datasets containing fires information in Cote D'Ivoire from December 2011 April 2012.
To properly understand and model animal embryogenesis it is crucial to obtain detailed measurements, both in time space, about their gene expression domains cell dynamics. Such challenge has been confronted recent years by a surge of atlases which integrate statistically relevant number different individuals get robust, complete information spatiotemporal locations patterns. This paper will discuss the fundamental image analysis strategies required build such models most common problems...
Obtaining the complete cell lineage tree of an embryo's development is a very appealing and ambitious goal, but fortunately recent developments both in optical imaging digital image processing are bringing it closer. However, when embryos (sea urchin for this work) with high enough spatial resolution short time-step to make segmentation tracking possible, currently not possible specimen throughout its all embryogenesis. For reason interesting explore how trees extracted from two different...
Biological tissues achieve proper shape and ordered structures during development through responses to internal external signals, with mechanical cues playing a crucial role. These forces guide cellular organization, leading complex self-organizing that are foundational embryonic patterns. Emerging theories experiments suggest “topological morphogens” drive these processes. Despite the predominance of three-dimensional (3D) in biology, studying 3D remains challenging due limited model...
The reconstruction of the cell lineage tree early zebrafish embryogenesis requires use in-vivo microscopy imaging and image processing strategies. Second (SHG) third harmonic generation (THG) observations in unstained embryos allows to detect divisions membranes from 1-cell 1K-cell stage. In this article, we present an ad-hoc pipeline for tracking segmentation enabling until This methodology has been used obtain digital allowing generate a quantitative description with minute temporal...
Understanding the mechanisms by which zebrafish pectoral fin develops is expected to produce insights on how vertebrate limbs grow from a 2D cell layer 3D structure. Two have been proposed drive limb morphogenesis in tetrapods: growth-based with higher proliferation rate at distal tip of bud than proximal side, and directed behaviors that include elongation, division migration non-random manner. Based quantitative experimental biological data level individual cells whole developing organ, we...