Virtual Embryo

TS2

E1

E0

E2

E4

E6

E8

E10

E12

E14

E16

E18

Birth

E0E5E10E15BirthP7P56

TS20

E12· Digital condensations

Digital rays form in the handplate. Eye is pigmented. External nares form.

2samples

1/2anatomy delineated

OPT · 2Optical 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. imputed · 2Imputed — not measured. scRNA-seq cells placed into the eMouseAtlas anatomical mesh for this Theiler stage by canonical organ mapping. The cell-type-to-organ assignment is the imputed part; position within an organ is random, so organ-level structure is meaningful and sub-organ texture is not. Stereo-seq · 6Stereo-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 · 9

Stage-matched · not registered to atlas anatomy

imputed

Imputed · E12.0

205,001 cells · 39 genes

Spatial · mouse · stage TS20 · dated E12.0, staged TS20

Imputed — eMouseAtlas mesh + Qiu et al. 2024 (OMG) scRNA-seq

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imputed

Imputed · E12.25

321,031 cells · 39 genes

Spatial · mouse · stage TS20 · dated E12.25, staged TS20

Imputed — eMouseAtlas mesh + Qiu et al. 2024 (OMG) scRNA-seq

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Stereo-seq

mosta_e12_5_e1s1

51,365 cells · 27,810 genes

Spatial · mouse · stage TS20

Chen et al., Cell 2022 (MOSTA)

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Stereo-seq

mosta_e12_5_e1s2

47,436 cells · 27,393 genes

Spatial · mouse · stage TS20

Chen et al., Cell 2022 (MOSTA)

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Stereo-seq

mosta_e12_5_e1s3

49,908 cells · 17,337 genes

Spatial · mouse · stage TS20

Chen et al., Cell 2022 (MOSTA)

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Stereo-seq

mosta_e12_5_e1s4

55,295 cells · 27,330 genes

Spatial · mouse · stage TS20

Chen et al., Cell 2022 (MOSTA)

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Stereo-seq

mosta_e12_5_e1s5

45,669 cells · 26,837 genes

Spatial · mouse · stage TS20

Chen et al., Cell 2022 (MOSTA)

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Stereo-seq

mosta_e12_5_e2s1

23,640 cells · 26,688 genes

Spatial · mouse · stage TS20

Chen et al., Cell 2022 (MOSTA)

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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 TS20 · spans 16 stages

Qiu et al., Nature 2024 (OMG)

3D reference models

Histology plates · 34

Kaufman atlas, EMAPA-annotated · scroll →

Knowledge graph · TS20

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

scRNA-seq · Literature · Predictions — coming soon

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Hindlimb handplate

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.

Finger separation

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