Multimodal Atlas of Zebrafish Development

Zebrahub is a comprehensive atlas of zebrafish embryonic development that combines single-cell RNA sequencing and light-sheet microscopy. Its aim is to provide a complete cartography of cellular lineages in space, time, and state space, which is essential to understanding how an organism develops.

Our ultimate goal is to create high-quality multimodal reference datasets of vertebrate development and make them broadly available to the scientific community.

The atlas includes a high-resolution, single-embryo scRNAseq timecourse dataset covering 10 developmental stages from bud-stage to 10-day-old larvae, as well as image-based lineage reconstructions obtained from high-resolution light-sheet microscopy.

If you choose to use our data or tools, please cite the preprint and carefully read our data release policy. We welcome collaborative interactions on the project analyses, please contact us.

Zebrahub also provides open source instrument designs, software tools, and experimental protocols to help accelerate the adoption of these technologies and facilitate comprehension of vertebrate development.

Zebrahub - Multimodal Zebrafish Developmental Atlas Reveals the State Transition Dynamics of Late Vertebrate Pluripotent Axial Progenitors. Lange et al. BioRxiv 2023.

This work is led by the Royer Group in collaboration with CZ Biohub's Data Science and Genomics Platforms.