Browse by modality
Every dataset in the atlas, grouped by data type
Spatial transcriptomics
3-D cell-resolved spatial atlases. Cells live in physical embryo coordinates; toggle between Spatial and UMAP inside each viewer.
70 datasets
Stereo-seq
digiembryo_e7_5_rep1
13,168 cells · 17,172 genes
mouse · stage TS11
Xie et al., Cell 2025 (digital embryo)
Stereo-seq
digiembryo_e7_5_rep2
8,190 cells · 16,364 genes
mouse · stage TS11
Xie et al., Cell 2025 (digital embryo)
Stereo-seq
digiembryo_e7_75_rep1
20,935 cells · 18,455 genes
mouse · stage TS12
Xie et al., Cell 2025 (digital embryo)
Stereo-seq
digiembryo_e7_75_rep2
23,736 cells · 18,790 genes
mouse · stage TS12
Xie et al., Cell 2025 (digital embryo)
Stereo-seq
digiembryo_e8_0_rep1
11,048 cells · 16,636 genes
mouse · stage TS12
Xie et al., Cell 2025 (digital embryo)
Stereo-seq
digiembryo_e8_0_rep2
27,266 cells · 19,046 genes
mouse · stage TS12
Xie et al., Cell 2025 (digital embryo)
Stereo-seq
e11_5_embryo
6,993,667 cells · 21,717 genes
mouse · stage TS19
Qiu et al., Cell 2024 (Spateo)
Stereo-seq
e11_5_heart
98,966 cells · 19,746 genes
mouse · stage TS19
Qiu et al., Cell 2024 (Spateo)
Stereo-seq
e9_5_embryo
646,893 cells · 17,649 genes
mouse · stage TS15
Qiu et al., Cell 2024 (Spateo)
Stereo-seq
e9_5_heart
19,780 cells · 12,581 genes
mouse · stage E9.5
Qiu et al., Cell 2024 (Spateo)
MERFISH
merfish_e6_75
7,093 cells · 498 genes
mouse · stage TS9
Virtual Embryo Challenge training release
MERFISH
merfish_e7_25
13,295 cells · 498 genes
mouse · stage TS10
Virtual Embryo Challenge training release
MERFISH
merfish_e8_0
31,671 cells · 500 genes
mouse · stage TS12
Virtual Embryo Challenge training release
MERFISH
merfish_e8_25
58,716 cells · 500 genes
mouse · stage TS12
Virtual Embryo Challenge training release
MERFISH
merfish_e8_75
24,826 cells · 500 genes
mouse · stage TS13
Virtual Embryo Challenge training release
MERFISH
merfish_e9_5
53,742 cells · 500 genes
mouse · stage TS15
Virtual Embryo Challenge training release
MERFISH
merfish_e9_5_mab21l2_ko
50,294 cells · 500 genes
mouse · stage TS15
Virtual Embryo Challenge training release — Mab21l2 knockout
Stereo-seq
mosta_e10_5_e1s1
18,408 cells · 25,201 genes
mouse · stage TS17
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e10_5_e1s2
18,647 cells · 25,544 genes
mouse · stage TS17
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e10_5_e1s3
18,670 cells · 25,647 genes
mouse · stage TS17
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e10_5_e2s1
8,494 cells · 22,385 genes
mouse · stage TS17
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e11_5_e1s1
30,124 cells · 26,854 genes
mouse · stage TS19
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e11_5_e1s2
30,756 cells · 25,485 genes
mouse · stage TS19
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e11_5_e1s3
27,455 cells · 25,741 genes
mouse · stage TS19
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e11_5_e1s4
30,775 cells · 25,798 genes
mouse · stage TS19
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e12_5_e1s1
51,365 cells · 27,810 genes
mouse · stage TS20
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e12_5_e1s2
47,436 cells · 27,393 genes
mouse · stage TS20
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e12_5_e1s3
49,908 cells · 17,337 genes
mouse · stage TS20
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e12_5_e1s4
55,295 cells · 27,330 genes
mouse · stage TS20
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e12_5_e1s5
45,669 cells · 26,837 genes
mouse · stage TS20
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e12_5_e2s1
23,640 cells · 26,688 genes
mouse · stage TS20
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e13_5_e1s1
77,369 cells · 28,408 genes
mouse · stage TS21
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e13_5_e1s2
64,584 cells · 28,208 genes
mouse · stage TS21
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e13_5_e1s3
84,811 cells · 27,841 genes
mouse · stage TS21
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e13_5_e1s4
73,168 cells · 27,732 genes
mouse · stage TS21
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e14_5_e1s1
102,519 cells · 28,463 genes
mouse · stage TS22
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e14_5_e1s2
102,977 cells · 28,766 genes
mouse · stage TS22
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e14_5_e1s3
92,928 cells · 18,582 genes
mouse · stage TS22
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e14_5_e1s4
105,857 cells · 29,245 genes
mouse · stage TS22
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e14_5_e1s5
101,353 cells · 28,150 genes
mouse · stage TS22
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e14_5_e2s1
92,764 cells · 26,944 genes
mouse · stage TS22
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e14_5_e2s2
112,086 cells · 28,193 genes
mouse · stage TS22
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e15_5_e1s1
113,350 cells · 28,798 genes
mouse · stage TS23
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e15_5_e1s2
109,811 cells · 28,154 genes
mouse · stage TS23
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e15_5_e1s3
104,042 cells · 28,488 genes
mouse · stage TS23
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e15_5_e1s4
104,845 cells · 28,635 genes
mouse · stage TS23
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e15_5_e2s1
72,944 cells · 26,921 genes
mouse · stage TS23
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e1s1
121,767 cells · 28,204 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e1s2
120,842 cells · 28,930 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e1s3
155,741 cells · 28,579 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e1s4
135,973 cells · 29,034 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e1s5
152,559 cells · 28,291 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s1
59,125 cells · 27,831 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s10
114,026 cells · 28,160 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s11
109,399 cells · 27,945 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s12
94,733 cells · 27,588 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s13
77,748 cells · 27,739 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s2
73,922 cells · 27,762 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s3
110,755 cells · 28,118 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s4
99,212 cells · 27,782 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s5
132,481 cells · 28,555 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s6
137,209 cells · 28,144 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s7
155,159 cells · 28,257 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s8
120,854 cells · 28,701 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e16_5_e2s9
129,425 cells · 28,878 genes
mouse · stage TS24
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e9_5_e1s1
5,913 cells · 25,568 genes
mouse · stage TS15
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e9_5_e2s1
5,292 cells · 23,756 genes
mouse · stage TS15
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e9_5_e2s2
4,356 cells · 24,107 genes
mouse · stage TS15
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e9_5_e2s3
5,059 cells · 24,238 genes
mouse · stage TS15
Chen et al., Cell 2022 (MOSTA)
Stereo-seq
mosta_e9_5_e2s4
5,797 cells · 23,398 genes
mouse · stage TS15
Chen et al., Cell 2022 (MOSTA)
Single-cell embeddings
UMAP / embedding atlases without spatial coordinates. Each card opens the full developmental time-lapse; use the time slider inside the viewer to focus on a specific stage.
3 datasets
Multiome RNAChallenge · E8.5 Multiome RNA
16,787 cells · 32,285 genes
mouse · TS12 – TS12 (1 stages)
Virtual Embryo Challenge training release
Multiome RNAChallenge · E9.5 Multiome RNA
17,057 cells · 32,285 genes
mouse · TS15 – TS15 (1 stages)
Virtual Embryo Challenge training release
sci-RNA-seq3Mouse prenatal time-lapse · whole atlas
11,441,407 cells · 45,525 genes
mouse · TS12 – TS27 (16 stages)
Qiu et al., Nature 2024 (OMG)
Anatomical references
Whole-mount OPT / histology with Theiler-staged 3-D reconstructions and Kaufman plate annotations.
72 samples · 1027 plates