Virtual Embryo

TS2

E1

E0

E2

E4

E6

E8

E10

E12

E14

E16

E18

Birth

E0E5E10E15BirthP7P56

TS10

E7· Amnion forms

Three germ layers established. Extra-embryonic membranes (amnion, allantois) emerge.

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. imputed · 1Imputed — 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 · 2

Stage-matched · not registered to atlas anatomy

MERFISH

merfish_e7_25

13,295 cells · 498 genes

Spatial · mouse · stage TS10

Virtual Embryo Challenge training release

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imputed

Imputed · E6.75

2,075 cells · 39 genes

Spatial · mouse · stage TS10 · dated E6.75, staged TS10