Virtual Embryo Atlas

Developmental timeline

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

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Timeline Modality

TS25

E16.5· Long whiskers

Long vibrissae. Lung saccular development. Brown adipose tissue forms.

4samples

2/4anatomy 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. OPT · 2Optical 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. imputed · 3Imputed — 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 · 18Stereo-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 · 22

Stage-matched · not registered to atlas anatomy

Imputed · E16.0

205,343 cells · 39 genes

Spatial · mouse · stage TS25 · dated E16.0, staged TS25

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

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Imputed · E16.5

228,892 cells · 39 genes

Spatial · mouse · stage TS25

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

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Imputed · E16.75

222,748 cells · 39 genes

Spatial · mouse · stage TS25 · dated E16.75, staged TS25

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

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mosta_e16_5_e1s1

121,767 cells · 28,204 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e1s2

120,842 cells · 28,930 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e1s3

155,741 cells · 28,579 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e1s4

135,973 cells · 29,034 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e1s5

152,559 cells · 28,291 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s1

59,125 cells · 27,831 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s10

114,026 cells · 28,160 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s11

109,399 cells · 27,945 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s12

94,733 cells · 27,588 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s13

77,748 cells · 27,739 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s2

73,922 cells · 27,762 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s3

110,755 cells · 28,118 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s4

99,212 cells · 27,782 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s5

132,481 cells · 28,555 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s6

137,209 cells · 28,144 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s7

155,159 cells · 28,257 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s8

120,854 cells · 28,701 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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mosta_e16_5_e2s9

129,425 cells · 28,878 genes

Spatial · mouse · stage TS25

Chen et al., Cell 2022 (MOSTA)

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Mouse prenatal time-lapse · whole atlas · TS25

Mouse prenatal time-lapse · whole atlas

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

Single-cell · pre-filtered to TS25 · 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 · 73

Kaufman atlas, EMAPA-annotated · scroll →

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Knowledge graph · TS25

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

scRNA-seq · Literature · Predictions — coming soon

TS24

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.

TS26