Virtual Embryo Atlas

Developmental timeline

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

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Timeline Modality

TS24

E15.5· Ear pinna

External ear pinna obvious. Skin layers stratify.

5samples

1/5anatomy delineated

OPT · 4Optical 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 · 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. Stereo-seq · 5Stereo-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. 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 · 10

Stage-matched · not registered to atlas anatomy

Imputed · E15.0

215,781 cells · 39 genes

Spatial · mouse · stage TS24 · dated E15.0, staged TS24

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

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Imputed · E15.25

156,648 cells · 39 genes

Spatial · mouse · stage TS24 · dated E15.25, staged TS24

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

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Imputed · E15.5

215,284 cells · 39 genes

Spatial · mouse · stage TS24

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

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Imputed · E15.75

239,821 cells · 39 genes

Spatial · mouse · stage TS24 · dated E15.75, staged TS24

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

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mosta_e15_5_e1s1

113,350 cells · 28,798 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

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mosta_e15_5_e1s2

109,811 cells · 28,154 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

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mosta_e15_5_e1s3

104,042 cells · 28,488 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

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mosta_e15_5_e1s4

104,845 cells · 28,635 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

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mosta_e15_5_e2s1

72,944 cells · 26,921 genes

Spatial · mouse · stage TS24

Chen et al., Cell 2022 (MOSTA)

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Mouse prenatal time-lapse · whole atlas · TS24

Mouse prenatal time-lapse · whole atlas

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

Single-cell · pre-filtered to TS24 · spans 16 stages

Qiu et al., Nature 2024 (OMG)

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3D reference models

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histologymeshlabels

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Histology plates · 79

Kaufman atlas, EMAPA-annotated · scroll →

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Knowledge graph · TS24

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

scRNA-seq · Literature · Predictions — coming soon

TS23

Eyelids closing

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.

TS25