Fig. 1

Fig. 1 Zebrahub—multimodal zebrafish developmental atlas (A) Zebrahub’s scRNA-seq experimental pipeline for single-zebrafish-embryo single-cell RNA sequencing across developmental stages (dpf, days post-fertilization; hpf, hours post-fertilization). From left to right, we show: first, the number of cells per time point and replicates. Second, an example UMAP for a 14 hpf embryo transcriptome colored by cell type (3,862 cells total). Third, Zebrahub’s web portal allows the exploration of scRNA-seq data online. (B) UMAP representation of the entire dataset of 40 single-embryo transcriptomes colored by developmental stage (120,000 total cells). (C) Same but colored by annotated cell types. (D) Maximum intensity projections of a 12-h light-sheet live imaging of a zebrafish embryo expressing histone-mCherry (cyan) and mezzo-GFP (magenta). Arrows indicate the mezzo-positive cells. (E) Similar imaging but on a transgenic embryo expressing the photoconvertible protein Dendra2. Photoconverted cells are in red (blue arrows). (F) Overview of DaXi, a high-resolution, large field-of-view and multi-view single-objective light-sheet microscope. (G) Computational pipeline for image processing and nuclei tracking applied to images of a histone-mCherry zebrafish embryo acquired with our DaXi microscope (see STAR Methods). (H) Screenshot of the in silico fate-mapping napari plugin available as part of Zebrahub (Methods S1).