Virtual Embryo

TS2

E1

E0

E2

E4

E6

E8

E10

E12

E14

E16

E18

Birth

E0E5E10E15BirthP7P56

TS12

E8· Neural folds

Neural folds elevate. First somites form. Cardiac crescent fuses to a tube.

4samples

1/4anatomy delineated

OPT · 1Optical 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 · 3Histology — 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 · 4Stereo-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. 10x Chromium v2/v3 + Smart-seq2 · 110x Chromium v2/v3 + Smart-seq2 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 · 6

Stage-matched · not registered to atlas anatomy

Stereo-seq

digiembryo_e7_75_rep1

20,935 cells · 18,455 genes

Spatial · mouse · stage TS12

Xie et al., Cell 2025 (digital embryo)

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Stereo-seq

digiembryo_e7_75_rep2

23,736 cells · 18,790 genes

Spatial · mouse · stage TS12

Xie et al., Cell 2025 (digital embryo)

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Stereo-seq

digiembryo_e8_0_rep1

11,048 cells · 16,636 genes

Spatial · mouse · stage TS12

Xie et al., Cell 2025 (digital embryo)

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Stereo-seq

digiembryo_e8_0_rep2

27,266 cells · 19,046 genes

Spatial · mouse · stage TS12

Xie et al., Cell 2025 (digital embryo)

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10x Chromium v2/v3 + Smart-seq2

Extended Mouse Atlas · E6.5–E9.5 gastrulation + early organogenesis

430,339 cells · 27,669 genes (full atlas)

Single-cell · pre-filtered to TS12 · spans 7 stages

Imaz-Rosshandler et al., Development 2024 (Extended Mouse Atlas)

Open UMAP for TS12 →

sci-RNA-seq3

Mouse prenatal time-lapse · whole atlas

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

Single-cell · pre-filtered to TS12 · spans 16 stages

Qiu et al., Nature 2024 (OMG)

Open UMAP for TS12 →

3D reference models

OPT

EMA145

· Head of embryo cultured from TS 10 (LSEB)

Histology plates · 51

Kaufman atlas, EMAPA-annotated · scroll →

Knowledge graph · TS12

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

scRNA-seq · Literature · Predictions — coming soon

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Neural plate

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.

5–8 somites; turning begins

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