Virtual EmbryoVirtual Embryo
Virtual Embryo Atlas
HumanMouse

Developmental timeline

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

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TimelineModality
TS1
TS1
E0.5
1-cell
TS2
TS2
E1
2-cell
TS3
TS3
E2
4-16 cell
TS4
TS4
E3
morula → blastocyst
TS5
TS5
E4
late blastocyst
TS6
TS6
E4.5
attaching blastocyst
TS71
TS7
E5
egg cylinder
TS81
TS8
E6
prestreak
TS92
TS9
E6.5
streak
TS103
TS10
E7
amnion
TS115
TS11
E7.5
neural plate
TS1210
TS12
E8
neural folds
TS134
TS13
E8.5
5-8 somites
TS143
TS14
E9
9-12 somites
TS1516
TS15
E9.5
13-20 somites
TS166
TS16
E10
forelimb buds
TS178
TS17
E10.5
hindlimb buds
TS187
TS18
E11
handplate
TS1915
TS19
E11.5
hindlimb handplate
TS209
TS20
E12
digital rays
TS217
TS21
E13.5
finger separation
TS229
TS22
E14
eyelid formation
TS2321
TS23
E15
eyelids closing
TS2424
TS24
E15.5
ear pinna
TS255
TS25
E16.5
long whiskers
TS262
TS26
E17.5
body hair
TS271
TS27
E18.5
pre-birth
P7
P7
P7
postnatal day 7
P56
P56
P56
adult (8 weeks)
E0
E2
E4
E6
E8
E10
E12
E14
E16
E18
Birth
E0E5E10E15BirthP7P56

TS10

E7· Amnion forms

Three germ layers established. Extra-embryonic membranes (amnion, allantois) emerge.

2samples
1/2anatomy delineated
histology · 2Histology — 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. 10x Chromium v2/v3 + Smart-seq2 · 110x Chromium v2/v3 + Smart-seq2
Transcriptomics data · 1
Stage-matched · not registered to atlas anatomy
Extended Mouse Atlas · E6.5–E9.5 gastrulation + early organogenesis · TS1010x 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 TS10 · spans 7 stages
Imaz-Rosshandler et al., Development 2024 (Extended Mouse Atlas)
Open UMAP for TS10 →
3D reference models
histologymeshlabels
EMA10
2×2×2 μm
Open viewer →
histology
EMA224
2×2×2 μm
Open viewer →
Histology plates · 31
Kaufman atlas, EMAPA-annotated · scroll →
ds_10283_1000Transverse3 ann
Plate 04o
TS10
ds_10283_1001Transverse3 ann
Plate 04p
TS10
ds_10283_971Transverse6 ann
Plate 03a
TS9 · TS10
ds_10283_972Transverse3 ann
Plate 03b
TS9 · TS10
ds_10283_973Transverse8 ann
Plate 03c
TS9 · TS10
ds_10283_974Transverse3 ann
Plate 03d
TS9 · TS10
ds_10283_975Transverse2 ann
Plate 03e
TS9 · TS10
ds_10283_976Transverse4 ann
Plate 03f
TS9 · TS10
ds_10283_977Transverse2 ann
Plate 03g
TS9 · TS10
ds_10283_978Transverse5 ann
Plate 03h
TS9 · TS10
ds_10283_979Transverse6 ann
Plate 03i
TS9 · TS10
ds_10283_980Transverse1 ann
Plate 03j
TS9 · TS10
ds_10283_981Transverse4 ann
Plate 03k
TS9 · TS10
ds_10283_982Transverse1 ann
Plate 03l
TS9 · TS10
ds_10283_983Transverse4 ann
Plate 03m
TS9 · TS10
ds_10283_984Transverse1 ann
Plate 03n
TS9 · TS10
ds_10283_985Transverse3 ann
Plate 03o
TS9 · TS10
ds_10283_986Transverse1 ann
Plate 04a
TS10
ds_10283_987Transverse2 ann
Plate 04b
TS10
ds_10283_988Transverse4 ann
Plate 04c
TS10
ds_10283_989Transverse4 ann
Plate 04d
TS10
ds_10283_990Transverse3 ann
Plate 04e
TS10
ds_10283_991Transverse4 ann
Plate 04f
TS10
ds_10283_992Transverse3 ann
Plate 04g
TS10
ds_10283_993Transverse4 ann
Plate 04h
TS10
ds_10283_994Transverse3 ann
Plate 04i
TS10
ds_10283_995Transverse3 ann
Plate 04j
TS10
ds_10283_996Transverse4 ann
Plate 04k
TS10
ds_10283_997Transverse1 ann
Plate 04l
TS10
ds_10283_998Transverse3 ann
Plate 04m
TS10
ds_10283_999Transverse2 ann
Plate 04n
TS10
Knowledge graph · TS10
EMAPA / CL-anchored · drag to rotate, scroll to zoom
scRNA-seq · Literature · Predictions — coming soon
←TS9
Previous
TS9E6.5
Streak — gastrulation begins
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.

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E7.5TS11
Neural plate
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