A5010017042- Cell Image Analysis Techniques
- Zebrafish Biomedical Research Applications
- Image Processing Techniques and Applications
- Single-cell and spatial transcriptomics
- Advanced Fluorescence Microscopy Techniques
- Water Quality Monitoring Technologies
- Genetics, Bioinformatics, and Biomedical Research
- Congenital heart defects research
- Digital Holography and Microscopy
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- RNA modifications and cancer
- Hemispheric Asymmetry in Neuroscience
- Gene Regulatory Network Analysis
- Developmental Biology and Gene Regulation
- AI in cancer detection
- Advanced Image and Video Retrieval Techniques
- Scientific Computing and Data Management
- Underwater Vehicles and Communication Systems
- Fish Ecology and Management Studies
- Immunotherapy and Immune Responses
- Bioinformatics and Genomic Networks
- Morphological variations and asymmetry
Chan Zuckerberg Initiative (United States)
2020-2024
Institut des Neurosciences Paris-Saclay
2019
Université Paris-Saclay
2019
Centre National de la Recherche Scientifique
2019
The promise of single-objective light-sheet microscopy is to combine the convenience standard microscopes with speed, coverage, resolution and gentleness microscopes. We present DaXi, a microscope design based on oblique plane illumination that achieves: (1) wider field view high-resolution imaging via custom remote focusing objective; (2) fast volumetric over larger volumes without compromising image quality or necessitating tiled acquisition; (3) fuller coverage for large samples...
A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals institutes across diverse modalities facing these have designed specification process (OME-NGFF) address needs. This paper brings together wide range those members describe cloud-optimized itself-OME-Zarr-along with tools data resources available today increase FAIR access remove barriers...
ABSTRACT Elucidating the developmental processes of organisms requires a comprehensive understanding cellular lineages in spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, dynamic atlas zebrafish embryonic development that integrates single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. This offers high-resolution in-depth insights into development, achieved through individual embryos across ten stages,...
The ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking the context vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling quantification transcription zebrafish, a model vertebrate. developed platform transgenic organisms, light sheet fluorescence microscopy, and optimized image analysis that enables visualization MS2 reporters. used these...
Tracking live cells across 2D, 3D, and multi-channel time-lapse recordings is crucial for understanding tissue-scale biological processes. Despite advancements in imaging technology, achieving accurate cell tracking remains challenging, particularly complex crowded tissues where segmentation often ambiguous. We present Ultrack, a versatile scalable cell-tracking method that tackles this challenge by considering candidate segmentations derived from multiple algorithms parameter sets. Ultrack...
A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals institutes across diverse modalities facing these have designed specification process (OME-NGFF) address needs. This paper brings together wide range those members describe cloud-optimized itself -- OME-Zarr along with tools data resources available today increase FAIR access remove...
Abstract Single-cell RNA sequencing is revolutionizing our understanding of cell state dynamics, allowing researchers to observe the progression individual cells’ transcriptomic profiles over time. Among computational techniques used predict future cellular states, velocity has emerged as a predominant tool for modeling transcriptional dynamics. leverages mRNA maturation process generate vectors that likely cell, offering insights into differentiation, aging, and disease progression....
Abstract In modern microscopy imaging systems, optical components are carefully designed to obtain diffraction-limited resolution. However, live of large biological samples rarely attains this limit because sample induced refractive index inhomogeneities that create unknown temporally variant aberrations. Importantly, these aberrations also spatially variant, thus making it challenging correct over wide fields view. Here, we present a framework for deep-learning based wide-field aberration...
Recent developments in Oblique Plane Microscopy (OPM) have shown that it can achieve high spatio-temporal resolution. Here we describe a single objective light-sheet microscope based on oblique plane illumination achieves: (i) large field of view and high-resolution imaging via custom remote focusing objective; (ii) fast volumetric by means stabilised stage scanning – novel modality extends the volume without compromising speed nor quality; (iii) multi-view alternating orientation detection...
In the past few decades, aquatic animals have become popular model organisms in biology, spurring a growing need for establishing facilities. Zebrafish are widely studied and relatively easy to culture using commercial systems. However, challenging aspect of maintaining facilities is animal feeding, which both time- resource-consuming. We developed an open-source fully automatic daily feeding system, Automatic Feeder (ZAF). ZAF reliable, provides standardized amount food every tank,...
During embryonic development, gene regulatory networks (GRNs) drive molecular differentiation of cell types. However, the temporal dynamics these remain poorly understood. Here, we present Zebrahub-Multiome, a comprehensive, time-resolved atlas zebrafish embryogenesis, integrating single-cell chromatin accessibility (scATAC-seq) and expression (scRNA-seq) from over 94,000 cells sampled across six key developmental stages (10 to 24 hours post-fertilization). Our analysis reveals early-stage...
In this work, we describe a method for large-scale 3D cell-tracking through segmentation selection approach. The proposed is effective at tracking cells across large microscopy datasets on two fronts: (i) It can solve problems containing millions of instances in terabyte-scale 3D+t datasets; (ii) achieves competitive results with or without deep learning, which requires annotated data, that scarce the fluorescence field. computes cell tracks and segments using hierarchy hypotheses selects...
While the vertebrate brain appears largely bilaterally symmetrical in humans, it presents local morphological Left-Right (LR) asymmetries as, for instance, petalia . Moreover, higher functions such as speech or handedness are asymmetrically localized cortex. How these generated remains unknown. Here, we reveal a striking parallel between control of bilateral symmetry and precursors vertebrae called somites, where “default” asymmetry is buffered by Retinoic Acid (RA) signaling. This mechanism...
In the past few decades, aquatic animals have become popular model organisms in biology, spurring a growing need for establishing facilities. Zebrafish are widely studied and relatively easy to culture using commercial systems. However, challenging aspect of maintaining facilities is animal feeding, which both time- resource-consuming. We developed an open-source fully automatic daily feeding system, Automatic Feeder (ZAF). ZAF reliable, provides standardized amount food every tank,...