Virtual Embryo Atlas

Developmental timeline

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

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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. seqFISH · 1seqFISH 10x Chromium v2/v3 + Smart-seq2 · 110x Chromium v2/v3 + Smart-seq2 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 · 3

Stage-matched · not registered to atlas anatomy

lohoff_seqfish_e8_5

57,536 cells · 351 genes

Spatial · mouse · stage E8.5–E8.75

Lohoff et al., Nature Biotechnology 2022 (Marioni Lab)

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Extended Mouse Atlas · E6.5–E9.5 gastrulation + early organogenesis · TS13

10x Chromium v2/v3 + Smart-seq2

Extended Mouse Atlas · E6.5–E9.5 gastrulation + early organogenesis

430,339 cells · 27,669 genes (full atlas)

Single-cell · pre-filtered to TS13 · spans 7 stages

Imaz-Rosshandler et al., Development 2024 (Extended Mouse Atlas)

Open UMAP for TS13 →

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

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Histology plates · 92

Kaufman atlas, EMAPA-annotated · scroll →

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Knowledge graph · TS13

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

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