Virtual Embryo Atlas

Developmental timeline

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

Timeline Modality

TS13

E8.5· 5–8 somites; turning begins

Embryo turns from concave to convex. Heart begins to beat.

1samples

1/1anatomy delineated

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. 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 · TS13

Mouse prenatal time-lapse · whole atlas

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

Single-cell · pre-filtered to TS13 · spans 16 stages

Qiu et al., Nature 2024 (OMG)

Open UMAP for TS13 →

3D reference models

histologymeshlabels

Open viewer →

Histology plates · 92

Kaufman atlas, EMAPA-annotated · scroll →

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scRNA-seq · Literature · Predictions — coming soon

TS12

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.

TS14