MERFISHEYES
Interactive Zebrafish Embryo Single-Cell Atlas | scRNA-seq, scATAC-seq & MERFISH Visualization
Data by Wan et al.; imputed from scMultiomics data by Liu et al.
Link to resource: https://schier.merfisheyes.com/
Link to the single-molecule version: https://sm-schier.merfisheyes.com/
Circadian and sleep deprivation associated brain activity signatures
Link to publication: Joo et al, 2026
Link to resource: https://sleep-wake-atlas.scicore.unibas.ch/
URD R package
Single-cell Reconstruction of Branching Developmental Trajectories in Zebrafish Embryogenesis
The URD R package, fully processed zebrafish data to explore in URD, an online web version of the tree, and the raw data are available here.
Link to resource: http://www.schierlab.fas.harvard.edu/urd
A detailed protocol describing the use of Cas9 in zebrafish can be downloaded here.
CHOPCHOP
CHOPCHOP is a web tool for designing sgRNA target sites for CRISPR/Cas9 mutagenesis. It accepts gene IDs, pasted sequence or genomic coordinates as input, and can be used to target a large number of organisms.
Z-brain is an expandable open-source atlas containing molecular labels and definitions of anatomical regions within a standard coordinate space. It is based on the brain registration of hundreds of larval zebrafish.