Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis

This dataset supports a whole-embryo investigation of the spatial and
temporal regulation of gene expression during early zebrafish development.
It includes high-resolution weMERFISH measurements of 495 genes at
subcellular resolution across three developmental stages (50%
epiboly/early gastrula, 75% epiboly/mid gastrula, and 6-somite stage/early
organogenesis), together with imputed spatial expression patterns for
25,872 additional genes. For each embryo, the dataset provides cell-level
transcript counts, spatial coordinates, subcellular localization of
individual transcripts, and corresponding tissue and cluster annotations.
In addition, the dataset contains the MERFISH-FATE cell correspondence
tables that link fixed embryos to whole-embryo live imaging, enabling
analysis of gene expression changes in the context of cell movements and
lineage trajectories. These data collectively form a comprehensive spatial
multiomics atlas of zebrafish gastrulation and early organogenesis,
supporting studies of gene regulation, tissue patterning, boundary
formation, and the integration of molecular and morphogenetic processes.