Virtual Embryo Atlas

Developmental timeline

TS1 (fertilized egg) → P56 (adult) · click a stage to load samples

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Timeline Modality

TS15

E9.5· 13–20 somites

Forelimb field, branchial arches II–III, posterior neuropore still open.

7samples

2/7anatomy delineated

OPT · 7Optical 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. Stereo-seq · 7Stereo-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. MERFISH · 2MERFISH — combinatorial single-molecule FISH, ~100s of targeted genes at subcellular resolution. Multiome RNA · 1Multiome RNA 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 · 13

Stage-matched · not registered to atlas anatomy

53,742 cells · 500 genes

Spatial · mouse · stage TS15

Virtual Embryo Challenge training release

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merfish_e9_5_mab21l2_ko

50,294 cells · 500 genes

Spatial · mouse · stage TS15

Virtual Embryo Challenge training release — Mab21l2 knockout

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Imputed · E9.5

336,999 cells · 169 genes

Spatial · mouse · stage TS15

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

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Imputed · E9.75

633,746 cells · 169 genes

Spatial · mouse · stage TS15 · dated E9.75, staged TS15

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

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646,893 cells · 17,649 genes

Spatial · mouse · stage TS15

Qiu et al., Cell 2024 (Spateo)

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19,780 cells · 12,581 genes

Spatial · mouse · stage E9.5

Qiu et al., Cell 2024 (Spateo)

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mosta_e9_5_e1s1

5,913 cells · 25,568 genes

Spatial · mouse · stage TS15

Chen et al., Cell 2022 (MOSTA)

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mosta_e9_5_e2s1

5,292 cells · 23,756 genes

Spatial · mouse · stage TS15

Chen et al., Cell 2022 (MOSTA)

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mosta_e9_5_e2s2

4,356 cells · 24,107 genes

Spatial · mouse · stage TS15

Chen et al., Cell 2022 (MOSTA)

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mosta_e9_5_e2s3

5,059 cells · 24,238 genes

Spatial · mouse · stage TS15

Chen et al., Cell 2022 (MOSTA)

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mosta_e9_5_e2s4

5,797 cells · 23,398 genes

Spatial · mouse · stage TS15

Chen et al., Cell 2022 (MOSTA)

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Challenge · E9.5 Multiome RNA · TS15

Challenge · E9.5 Multiome RNA

17,057 cells · 32,285 genes (full atlas)

Single-cell · pre-filtered to TS15 · spans 1 stages

Virtual Embryo Challenge training release

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Mouse prenatal time-lapse · whole atlas · TS15

Mouse prenatal time-lapse · whole atlas

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

Single-cell · pre-filtered to TS15 · spans 16 stages

Qiu et al., Nature 2024 (OMG)

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3D reference models

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6.2×6.2×6.2 μm

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6.2×6.2×6.2 μm

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6.2×6.2×6.2 μm

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6.2×6.2×6.2 μm

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Histology plates · 80

Kaufman atlas, EMAPA-annotated · scroll →

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Knowledge graph · TS15

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

scRNA-seq · Literature · Predictions — coming soon

TS14

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.

TS16