Virtual Embryo Atlas
Browse by modality
Every dataset in the atlas, grouped by data type
Spatial transcriptomics
3-D cell-resolved spatial atlases. Cells live in physical embryo coordinates; toggle between Spatial and UMAP inside each viewer.
4 datasets
Stereo-seq
e11_5_embryo
6,993,667 cells · 21,717 genes
mouse · stage TS19
Qiu et al., Cell 2024 (Spateo)
Stereo-seq
e11_5_heart
98,966 cells · 19,746 genes
mouse · stage TS19
Qiu et al., Cell 2024 (Spateo)
Stereo-seq
e9_5_embryo
646,893 cells · 17,649 genes
mouse · stage TS15
Qiu et al., Cell 2024 (Spateo)
Stereo-seq
e9_5_heart
19,780 cells · 12,581 genes
mouse · stage E9.5
Qiu et al., Cell 2024 (Spateo)
Single-cell embeddings
UMAP / embedding atlases without spatial coordinates. Each card opens the full developmental time-lapse; use the time slider inside the viewer to focus on a specific stage.
1 datasets
Anatomical references
Whole-mount OPT / histology with Theiler-staged 3-D reconstructions and Kaufman plate annotations.
72 samples · 1027 plates