Virtual Embryo

TS2

E1

E0

E2

E4

E6

E8

E10

E12

E14

E16

E18

Birth

E0E5E10E15BirthP7P56

TS11

E7.5· Neural plate

Anterior neural plate appears. Heart field and somitic mesoderm specify.

2samples

1/2anatomy delineated

histology · 2Histology — 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 · 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. 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.

Transcriptomics data · 4

Stage-matched · not registered to atlas anatomy

Stereo-seq

digiembryo_e7_5_rep1

13,168 cells · 17,172 genes

Spatial · mouse · stage TS11

Xie et al., Cell 2025 (digital embryo)

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Stereo-seq

digiembryo_e7_5_rep2

8,190 cells · 16,364 genes

Spatial · mouse · stage TS11

Xie et al., Cell 2025 (digital embryo)

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imputed

Imputed · E7.25

13,537 cells · 39 genes

Spatial · mouse · stage TS11 · dated E7.25, staged TS11

Imputed — eMouseAtlas mesh + TOME scRNA-seq

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imputed

Imputed · E7.5

10,994 cells · 39 genes

Spatial · mouse · stage TS11

Imputed — eMouseAtlas mesh + TOME scRNA-seq

3D reference models

Histology plates · 50

Kaufman atlas, EMAPA-annotated · scroll →

Knowledge graph · TS11

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

scRNA-seq · Literature · Predictions — coming soon

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Amnion forms

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.

Neural folds

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