Virtual Embryo Atlas

Developmental timeline

TS1 (fertilized egg) → P56 (adult) · click a stage to load samples

Timeline Modality

E0

E2

E4

E6

E8

E10

E12

E14

E16

E18

Birth

E0E5E10E15BirthP7P56

TS15

E9.5· 13–20 somites

Forelimb field, branchial arches II–III, posterior neuropore still open.

7samples

2/7anatomy delineated

OPT · 7Optical Projection Tomography — a 3D scan of a chemically cleared embryo, captured by rotating it through 360° in a wide-field microscope. Isotropic voxels; raw bg = dark, tissue = bright. Stereo-seq · 2Stereo-seq (BGI) — DNB-array spatial transcriptomics with subcellular ~500 nm resolution. Captures whole-organ to whole-embryo sections; in the Spateo Cell 2024 atlas, 74 sections per embryo were aligned into a 3D cell-bin volume. sci-RNA-seq3 · 1sci-RNA-seq3 — high-throughput single-nucleus combinatorial-indexing RNA-seq (Shendure lab). The OMG mouse prenatal time-lapse profiled 11.4M nuclei across 45 developmental bins from E8 to P0 with this protocol.

Transcriptomics data · 3

Stage-matched · not registered to atlas anatomy

Stereo-seq

e9_5_embryo

646,893 cells · 17,649 genes

Spatial · mouse · stage TS15

Qiu et al., Cell 2024 (Spateo)

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Stereo-seq

e9_5_heart

19,780 cells · 12,581 genes

Spatial · mouse · stage E9.5

Qiu et al., Cell 2024 (Spateo)

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sci-RNA-seq3

Mouse prenatal time-lapse · whole atlas

11,441,407 cells · 45,525 genes (full atlas)

Single-cell · pre-filtered to TS15 · spans 16 stages

Qiu et al., Nature 2024 (OMG)

3D reference models

Histology plates · 80

Kaufman atlas, EMAPA-annotated · scroll →

scRNA-seq · Literature · Predictions — coming soon

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9–12 somites

About Theiler staging

Karl Theiler's staging system (1972) partitions prenatal development into 28 morphologically distinct steps. Virtual Embryo aligns all imagery, anatomy, and future spatial transcriptomics data to this axis.

Forelimb buds

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