Virtual Embryo Atlas

Developmental timeline

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

View

Timeline Modality

TS24

E15.5· Ear pinna

External ear pinna obvious. Skin layers stratify.

5samples

0/5anatomy delineated

OPT · 4Optical 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. histology · 1Histology — embryo physically embedded and microtomed into 1–7 µm sections, stained (Nissl / H&E), imaged, and reassembled into a 3D volume. High in-plane resolution, anisotropic voxels. Stereo-seq · 18Stereo-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 · 19

Stage-matched · not registered to atlas anatomy

mosta_e16_5_e1s1

121,767 cells · 28,204 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e1s2

120,842 cells · 28,930 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e1s3

155,741 cells · 28,579 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e1s4

135,973 cells · 29,034 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e1s5

152,559 cells · 28,291 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s1

59,125 cells · 27,831 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s10

114,026 cells · 28,160 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s11

109,399 cells · 27,945 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s12

94,733 cells · 27,588 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s13

77,748 cells · 27,739 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s2

73,922 cells · 27,762 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s3

110,755 cells · 28,118 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s4

99,212 cells · 27,782 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s5

132,481 cells · 28,555 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s6

137,209 cells · 28,144 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s7

155,159 cells · 28,257 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s8

120,854 cells · 28,701 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

mosta_e16_5_e2s9

129,425 cells · 28,878 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

Open viewer →

Mouse prenatal time-lapse · whole atlas · TS24

Mouse prenatal time-lapse · whole atlas

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

Single-cell · pre-filtered to TS24 · spans 16 stages

Qiu et al., Nature 2024 (OMG)

Open UMAP for TS24 →

3D reference models

Open viewer →

Open viewer →

Open viewer →

Open viewer →

histologylabels

Open viewer →

Histology plates · 79

Kaufman atlas, EMAPA-annotated · scroll →

Transverse26 ann

Transverse8 ann

Transverse10 ann

Transverse18 ann

Transverse17 ann

Transverse32 ann

Transverse22 ann

Transverse23 ann

Transverse23 ann

Transverse43 ann

Transverse16 ann

Transverse21 ann

Transverse16 ann

Transverse39 ann

Transverse16 ann

Transverse19 ann

Transverse20 ann

Transverse38 ann

Transverse25 ann

Transverse16 ann

Transverse16 ann

Transverse36 ann

Transverse20 ann

Transverse18 ann

Transverse15 ann

Transverse32 ann

Transverse27 ann

Transverse14 ann

Transverse12 ann

Transverse36 ann

Transverse19 ann

Transverse12 ann

Transverse15 ann

Transverse41 ann

Transverse19 ann

Transverse12 ann

Transverse10 ann

Transverse40 ann

Transverse15 ann

Transverse17 ann

Transverse18 ann

Transverse41 ann

Transverse13 ann

Transverse19 ann

Transverse16 ann

Transverse40 ann

Transverse15 ann

Transverse11 ann

Transverse9 ann

Transverse4 ann

Knowledge graph · TS24

EMAPA / CL-anchored · drag to rotate, scroll to zoom

scRNA-seq · Literature · Predictions — coming soon

TS23

Eyelids closing

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.

TS25