"Zebrahub – Multimodal Zebrafish Developmental Atlas Reveals the State-Transition Dynamics of Late-Vertebrate Pluripotent Axial Progenitors"

Date

Oct 13, 2023

Time

10:00 AM - 11:00 AM

Speaker

Loïc Alain Royer

Affiliation

Chan Zuckerberg Biohub, San Francisco

Language

en

Main Topic

Biologie

Host

Ivo Sbalzarini

Description

Elucidating the developmental processes of organisms requires a comprehensive understanding of cellular lineages in the spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, a dynamic atlas of zebrafish embryonic development that integrates single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. This atlas offers high-resolution and in-depth molecular insights into zebrafish development, achieved through the sequencing of individual embryos across ten developmental stages, complemented by trajectory reconstructions. Zebrahub also incorporates an interactive tool to navigate the complex cellular flows and lineages derived from light-sheet microscopy data, enabling in-silico fate mapping experiments. Finally, to demonstrate the versatility of our multi-modal resource, we utilize Zebrahub to provide fresh insights into the pluripotency of Neuro-Mesodermal Progenitors (NMPs). Our publicly accessible web-based platform, Zebrahub, is a foundational resource for studying developmental processes at both transcriptional and spatiotemporal levels, providing researchers with an integrated approach to exploring and analyzing the complexities of cellular lineages during zebrafish embryogenesis. This work was made possible by the development of a broad range of technologies developed by my team, such as the napari viewer, novel state-of-the-art fluorescence microscopes (DaXi), self-supervised learning for bioimaging (CytoSelf), fast and scalable image processing for light-sheet time-lapse data (DEXP), high-accuracy cell tracking at scale in developing embryos (ultrack), fast, robust, and user-friendly image denoising (Aydin), and more recently the use of large language models for accelerating the dissemination of bioimaging skills and methods (Omega).

Last modified: Oct 14, 2023, 7:39:57 AM