Virtual Embryo Atlas

Developmental timeline

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

Timeline Modality

TS18

E11· Forelimb handplate

AER active in limbs. Trigeminal ganglion prominent. Pinna of ear begins.

6samples

1/6anatomy delineated

OPT · 6Optical 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. 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 · 1

Stage-matched · not registered to atlas anatomy

Mouse prenatal time-lapse · whole atlas · TS18

Mouse prenatal time-lapse · whole atlas

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

Single-cell · pre-filtered to TS18 · spans 16 stages

Qiu et al., Nature 2024 (OMG)

Open UMAP for TS18 →

3D reference models

4.53×4.53×5.6 μm

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9.9×9.9×9.9 μm

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9.9×9.9×9.9 μm

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9.9×9.9×9.9 μm

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9.9×9.9×9.9 μm

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9.9×9.9×9.9 μm

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Histology plates · 81

Kaufman atlas, EMAPA-annotated · scroll →

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scRNA-seq · Literature · Predictions — coming soon

TS17

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.

Hindlimb handplate

TS19