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.
143 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)
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)
seqFISH
lohoff_seqfish_e8_5
57,536 cells · 351 genes
mouse · stage E8.5–E8.75
Lohoff et al., Nature Biotechnology 2022 (Marioni Lab)
Stereo-seq
hesta_cs12_13_e1s1
5,819 cells · 32,712 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e1s2
7,405 cells · 35,421 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e1s3
6,824 cells · 36,612 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e1s4
3,860 cells · 33,970 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e2s1
12,138 cells · 40,249 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e2s2
11,123 cells · 40,086 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e2s3
13,257 cells · 42,266 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e2s4
12,865 cells · 38,786 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e2s5
11,259 cells · 37,481 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e2s6
14,843 cells · 38,026 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e2s7
9,603 cells · 37,220 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_13_e2s8
8,906 cells · 38,410 genes
human · stage CS12-13
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_to_cs23_brain
231,318 cells · 25,474 genes
human · stage CS12
HESTA (Nature 2026)
Stereo-seq
hesta_cs12_to_cs23_heart
63,231 cells · 15,399 genes
human · stage CS12
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e1s1
18,374 cells · 41,231 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e1s2
21,014 cells · 40,752 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e1s3
20,637 cells · 41,490 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e1s4
22,476 cells · 40,846 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e2s1
16,470 cells · 42,580 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e2s10
22,203 cells · 39,623 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e2s2
17,782 cells · 41,775 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e2s3
19,800 cells · 43,042 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e2s4
16,872 cells · 41,287 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e2s5
21,129 cells · 41,613 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e2s6
19,662 cells · 40,893 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e2s7
23,195 cells · 41,385 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e2s8
19,803 cells · 40,804 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e2s9
18,797 cells · 40,069 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e3s1
25,535 cells · 43,051 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e3s2
31,576 cells · 42,396 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e3s3
32,816 cells · 41,539 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs14_15_e3s4
37,379 cells · 41,356 genes
human · stage CS14-15
HESTA (Nature 2026)
Stereo-seq
hesta_cs17_e1s1
44,531 cells · 43,559 genes
human · stage CS17
HESTA (Nature 2026)
Stereo-seq
hesta_cs17_e1s10
78,155 cells · 43,324 genes
human · stage CS17
HESTA (Nature 2026)
Stereo-seq
hesta_cs17_e1s2
47,670 cells · 44,532 genes
human · stage CS17
HESTA (Nature 2026)
Stereo-seq
hesta_cs17_e1s3
52,366 cells · 45,339 genes
human · stage CS17
HESTA (Nature 2026)
Stereo-seq
hesta_cs17_e1s4
59,423 cells · 45,516 genes
human · stage CS17
HESTA (Nature 2026)
Stereo-seq
hesta_cs17_e1s5
62,655 cells · 44,351 genes
human · stage CS17
HESTA (Nature 2026)
Stereo-seq
hesta_cs17_e1s6
56,279 cells · 46,371 genes
human · stage CS17
HESTA (Nature 2026)
Stereo-seq
hesta_cs17_e1s7
65,443 cells · 44,092 genes
human · stage CS17
HESTA (Nature 2026)
Stereo-seq
hesta_cs17_e1s8
66,586 cells · 44,254 genes
human · stage CS17
HESTA (Nature 2026)
Stereo-seq
hesta_cs17_e1s9
65,607 cells · 46,144 genes
human · stage CS17
HESTA (Nature 2026)
Stereo-seq
hesta_cs18_e1s1
77,312 cells · 46,688 genes
human · stage CS18
HESTA (Nature 2026)
Stereo-seq
hesta_cs18_e1s2
112,705 cells · 46,711 genes
human · stage CS18
HESTA (Nature 2026)
Stereo-seq
hesta_cs18_e1s3
132,277 cells · 47,028 genes
human · stage CS18
HESTA (Nature 2026)
Stereo-seq
hesta_cs18_e1s4
152,371 cells · 46,814 genes
human · stage CS18
HESTA (Nature 2026)
Stereo-seq
hesta_cs18_e1s5
161,900 cells · 45,872 genes
human · stage CS18
HESTA (Nature 2026)
Stereo-seq
hesta_cs18_e1s6
108,726 cells · 45,743 genes
human · stage CS18
HESTA (Nature 2026)
Stereo-seq
hesta_cs19_e1s1
147,865 cells · 51,924 genes
human · stage CS19
HESTA (Nature 2026)
Stereo-seq
hesta_cs19_e1s2
155,811 cells · 51,245 genes
human · stage CS19
HESTA (Nature 2026)
Stereo-seq
hesta_cs19_e1s3
160,662 cells · 52,304 genes
human · stage CS19
HESTA (Nature 2026)
Stereo-seq
hesta_cs19_e2s1
247,960 cells · 51,116 genes
human · stage CS19
HESTA (Nature 2026)
Stereo-seq
hesta_cs19_e2s2
247,783 cells · 51,257 genes
human · stage CS19
HESTA (Nature 2026)
Stereo-seq
hesta_cs19_e2s3
263,202 cells · 47,570 genes
human · stage CS19
HESTA (Nature 2026)
Stereo-seq
hesta_cs19_e2s4
263,815 cells · 48,476 genes
human · stage CS19
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e1s1
175,487 cells · 47,415 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e1s2
197,466 cells · 47,736 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e1s3
208,433 cells · 47,415 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e1s4
253,104 cells · 48,540 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e1s5
263,538 cells · 46,473 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e1s6
248,690 cells · 51,890 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e1s7
265,988 cells · 52,248 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e2s1
265,120 cells · 53,727 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e2s2
289,486 cells · 52,809 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e2s3
286,933 cells · 53,786 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs20_e2s4
269,429 cells · 54,056 genes
human · stage CS20
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e1s1
554,306 cells · 52,983 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e1s2
539,831 cells · 53,185 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e1s3
531,126 cells · 52,125 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e2s1
662,769 cells · 49,848 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e2s10
733,507 cells · 52,365 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e2s2
655,242 cells · 49,753 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e2s3
637,053 cells · 51,169 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e2s4
633,615 cells · 50,065 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e2s5
671,089 cells · 50,470 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e2s6
727,736 cells · 51,014 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e2s7
712,097 cells · 50,813 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e2s8
825,115 cells · 53,311 genes
human · stage CS23
HESTA (Nature 2026)
Stereo-seq
hesta_cs23_e2s9
747,172 cells · 52,509 genes
human · stage CS23
HESTA (Nature 2026)
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.
2 datasets
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)
10x Chromium v2/v3 + Smart-seq2Extended Mouse Atlas · E6.5–E9.5 gastrulation + early organogenesis
430,339 cells · 27,669 genes
mouse · TS9 – TS15 (7 stages)
Imaz-Rosshandler et al., Development 2024 (Extended Mouse Atlas)
Anatomical references
Whole-mount OPT / histology with Theiler-staged 3-D reconstructions and Kaufman plate annotations.
72 samples · 1027 plates