Virtual Embryo Atlas

Developmental timeline

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

Timeline Modality

TS23

E15· Eyelids closing

Body coat begins. Liver hematopoiesis peaks.

15samples

3/15anatomy delineated

OPT · 11Optical 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. histology · 4Histology — 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 · TS23

Mouse prenatal time-lapse · whole atlas

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

Single-cell · pre-filtered to TS23 · spans 16 stages

Qiu et al., Nature 2024 (OMG)

Open UMAP for TS23 →

3D reference models

0.34×0.34×7 μm

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histologymeshlabels

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17.5×17.5×17.5 μm

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17.5×17.5×17.5 μm

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Histology plates · 80

Kaufman atlas, EMAPA-annotated · scroll →

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scRNA-seq · Literature · Predictions — coming soon

TS22

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.

TS24