Virtual Embryo Atlas

Developmental timeline

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

Timeline Modality

TS22

E14· Eyelids begin

Distinct fingers and toes. Hair follicles, mammary buds appear.

1samples

0/1anatomy 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. 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 · TS22

Mouse prenatal time-lapse · whole atlas

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

Single-cell · pre-filtered to TS22 · spans 16 stages

Qiu et al., Nature 2024 (OMG)

Open UMAP for TS22 →

3D reference models

Open viewer →

Histology plates · 130

Kaufman atlas, EMAPA-annotated · scroll →

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scRNA-seq · Literature · Predictions — coming soon

TS21

Finger separation

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.

Eyelids closing

TS23