Virtual Embryo

TS2

E1

E0

E2

E4

E6

E8

E10

E12

E14

E16

E18

Birth

E0E5E10E15BirthP7P56

TS9

E6.5· Streak — gastrulation begins

Primitive streak forms at the posterior. Mesoderm and definitive endoderm ingress.

1samples

1/1anatomy delineated

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. imputed · 4Imputed — 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. MERFISH · 1MERFISH — combinatorial single-molecule FISH, ~100s of targeted genes at subcellular resolution.

Transcriptomics data · 5

Stage-matched · not registered to atlas anatomy

MERFISH

merfish_e6_75

7,093 cells · 498 genes

Spatial · mouse · stage TS9

Virtual Embryo Challenge training release

Spatial · mouse · stage TS09 · dated E5.25, staged TS9

Imputed — eMouseAtlas mesh + TOME scRNA-seq

Spatial · mouse · stage TS09 · dated E5.5, staged TS9

Imputed — eMouseAtlas mesh + TOME scRNA-seq

Spatial · mouse · stage TS09 · dated E6.25, staged TS9

Imputed — eMouseAtlas mesh + TOME scRNA-seq

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imputed

Imputed · E6.5

4,444 cells · 39 genes

Spatial · mouse · stage TS09

Imputed — eMouseAtlas mesh + TOME scRNA-seq

3D reference models

Histology plates · 15

Kaufman atlas, EMAPA-annotated · scroll →

Knowledge graph · TS9

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

scRNA-seq · Literature · Predictions — coming soon

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Prestreak

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.

Amnion forms

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