scAtria single-cell spatial atlas resource

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View by ?Dataset view shows one row per deployed dataset. Sample view shows one row per sample and is better for organ, disease, and spatial availability checks.
Dataset Sample
View mode ?Cards are for quick scanning. Tables are denser and better for comparison, sorting, and column customization.
Card Table
Search?Search is user-initiated: type one keyword or several comma-separated keywords, then click Search keyword. Commas search alternatives, for example breast cancer, HNSCC, Xenium.
Filter scope 61 matches · dataset view
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Customized columns 8
Dataset table columns Selections persist in the URL and manifest download.
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Modality: Spatial transcriptomics × 61 matches 49 curated
Dataset Organs ?For mixed datasets, fractions show sample counts per organ. Disease state ?Broad public sample state summarized across the dataset. Technique Samples Cells ?Number of individually resolved single-cell observations included for the dataset. Spatial module ?Spatial availability is summarized from module- and tier-level outputs for the dataset. Curation ?Curated records have standardized ontology labels and normalized metadata. Source records are ingested but not fully standardized yet.
10x Genomics Atera showcase
Atera_10xGenomics__Atera
Breast 1/2 Uterus/Cervix 1/2
Primary cancer 2
Atera 2 887,633
0/2
 Curated
10x Genomics Visium HD p2 TMA showcase
VisiumHD_p2_TMA__Visium_HD
Breast 36
Primary cancer 36
Visium HD 36 117,494
36/36
 Curated
10x Genomics Visium HD p2 TissueArray showcase
VisiumHD_p2_TissueArray__Visium_HD
Breast 1/3 Large intestine 1/3 Lung 1/3
Primary cancer 3
Visium HD 3 506,235
0/3
 Curated
10x Genomics Visium HD p2 WholeSlide showcase
VisiumHD_p2_WholeSlide__Visium_HD
Heart 1/3 Large intestine 2/3
Primary cancer 2/3 Healthy/control 1/3
Visium HD 3 1,729,339
1/3
 Curated
10x Genomics Visium HD showcase
Visium_HD_10xGenomics__Visium_HD
Breast 3/24 Kidney 1/24 Large intestine 5/24 Lung 5/24 Lymphoid tissue 2/24 Ovary 5/24 Pancreas 2/24 Prostate 1/24
Primary cancer 20/24 Healthy/control 4/24
Visium HD 24 5,379,712
3/24
 Curated
10x Genomics Xenium Prime 5K showcase
Xenium5k_10xGenomics__Xenium
Breast 1/9 Lung 1/9 Lymphoid tissue 1/9 Ovary 3/9 Prostate 1/9 Skin 1/9 Uterus/Cervix 1/9
Primary cancer 8/9 Non-cancer disease 1/9
Xenium 9 4,598,042
0/9
 Curated
Bruker CosMx 1k FFPE showcase
CosMx1k_Bruker__CosMx_SMI
Liver 2
Healthy/control 1/2 Primary cancer 1/2
CosMx 2 793,318
0/2
 Curated
Bruker CosMx 6k FFPE showcase
CosMx6k_Bruker__CosMx_SMI
Brain 1/2 Lymphoid tissue 1/2
Healthy/control 2
CosMx 2 2,041,632
0/2
 Curated
Bruker CosMx WTx FFPE showcase
CosMxWTx_Bruker__CosMx_SMI
Brain 1/9 Breast 2/9 Kidney 1/9 Large intestine 1/9 Pancreas 3/9 Skin 1/9
Primary cancer 5/9 Healthy/control 4/9
CosMx 9 2,878,028
2/9
 Curated
CRC_41986711 · CosMx SMI / NanoString SMI
CRC_41986711__CosMx_SMI
Large intestine 352
Primary cancer 352
CosMx 352 629,446
350/352
 Curated
CastlemanDisease_40593805 · Xenium
CastlemanDisease_40593805__Xenium
Lymphoid tissue 18
Non-cancer disease 18
Xenium 18 1,299,746
12/18
 Curated
CutaneousLeishmaniasis_40371647 · CosMx SMI / NanoString SMI
CutaneousLeishmaniasis_40371647__CosMx_SMI
Skin 4
Non-cancer disease 4
CosMx 4 130,801
4/4
 Curated
DKD_42056516 · CosMx SMI / NanoString SMI
DKD_42056516__CosMx_SMI
Kidney 48
Non-cancer disease 36/48 Healthy/control 12/48
CosMx 48 3,386,822
37/48
 Curated
DKD_42056516 · Xenium
DKD_42056516__Xenium
Kidney 16
Non-cancer disease 13/16 Healthy/control 3/16
Xenium 16 951,040
12/16
 Curated
DLBCL_41874448 · CosMx SMI / NanoString SMI
DLBCL_41874448__CosMx_SMI
Lymphoid tissue 56
Primary cancer 56
CosMx 56 182,646
56/56
 Curated
HGSC_39179931 · CosMx SMI / NanoString SMI
HGSC_39179931__CosMx_SMI
Ovary 116/166 Peritoneum 50/166
Metastatic cancer 50/166 Primary cancer 116/166
CosMx 166 1,724,825
162/166
 Curated
HGSC_39179931 · MERFISH / MERSCOPE
HGSC_39179931__MERFISH
Ovary 4
Primary cancer 4
MERFISH 4 425,578
2/4
 Curated
HGSC_39179931 · Xenium
HGSC_39179931__Xenium
Ovary 16/32 Peritoneum 16/32
Metastatic cancer 16/32 Primary cancer 16/32
Xenium 32 447,874
32/32
 Curated
HNSCC_41616773 · Other ST
HNSCC_41616773__Other_ST
Lymph node metastasis 46/137 Lymphoid tissue 91/137
Primary cancer 73/137 Metastatic cancer 46/137 Healthy/control 18/137
Other ST 137 1,156,046
136/137
 Curated
IBD_42049732 · CosMx SMI / NanoString SMI
IBD_42049732__CosMx_SMI
Large intestine 34
Non-cancer disease 34
CosMx 34 43,034
34/34
 Curated
Intestine_39843748 · MERFISH / MERSCOPE
Intestine_39843748__MERFISH
Large intestine 2
Healthy/control 2
MERFISH 2 470,081
0/2
 Curated
Intestine_39843748 · Xenium
Intestine_39843748__Xenium
Large intestine 16
Healthy/control 16
Xenium 16 2,814,759
4/16
 Curated
LiverCancer_41723121 HCC cohort · CosMx SMI / NanoString SMI
HCC_41723121__CosMx_SMI
Liver 9
Primary cancer 9
CosMx 9 1,446,124
4/9
 Curated
LiverCancer_41723121 iCCA cohort · CosMx SMI / NanoString SMI
ICC_41723121__CosMx_SMI
Liver 6
Primary cancer 6
CosMx 6 901,465
3/6
 Curated
MERFISH 500-plex Vizgen showcase
MERFISH_500_Vizgen__MERFISH
Breast 1/18 Large intestine 2/18 Liver 2/18 Lung 2/18 Ovary 4/18 Prostate 2/18 Skin 2/18 Uterus/Cervix 3/18
Primary cancer 18
MERFISH 18 10,196,835
1/18
 Curated
MERFISH 815-plex Vizgen showcase
MERFISH_815_Vizgen__MERFISH
Breast 5/6 Large intestine 1/6
Primary cancer 6
MERFISH 6 1,051,006
5/6
 Curated
MERFISH 960-plex Vizgen showcase
MERFISH_960_Vizgen__MERFISH
Brain 3
Non-cancer disease 2/3 Healthy/control 1/3
MERFISH 3 394,181
1/3
 Curated
Melanoma_40148341 · CosMx SMI / NanoString SMI
Melanoma_40148341__CosMx_SMI
Skin 25
Primary cancer 25
CosMx 25 56,761
25/25
 Curated
Neocortex_39779846 · MERFISH / MERSCOPE
Neocortex_39779846__MERFISH
Brain 6
Healthy/control 6
MERFISH 6 404,030
5/6
 Curated
NormalSkin_41872488 · MERFISH / MERSCOPE
NormalSkin_41872488__MERFISH
Skin 114
Healthy/control 114
MERFISH 114 1,201,886
113/114
 Curated
PDAC_39227743 · CosMx SMI / NanoString SMI
PDAC_39227743__CosMx_SMI
Pancreas 16
Primary cancer 16
CosMx 16 717,493
0/16
 Curated
PDAC_40269162 · CosMx SMI / NanoString SMI
PDAC_40269162__CosMx_SMI
Pancreas 90
Primary cancer 90
CosMx 90 82,348
84/90
 Curated
PulmonaryFibrosis_39901013 · Xenium
PulmonaryFibrosis_39901013__Xenium
Lung 45
Non-cancer disease 35/45 Healthy/control 10/45
Xenium 45 790,934
45/45
 Curated
SCN_41720090 · MERFISH / MERSCOPE
SCN_41720090__MERFISH
Brain 1
Healthy/control 1
MERFISH 1 6,953
1/1
 Curated
SCN_41720090 · Visium HD
SCN_41720090__Visium_HD
Brain 1
Healthy/control 1
Visium HD 1 16,123
1/1
 Curated
SPATCH_41107232 · CosMx SMI / NanoString SMI
SPATCH_41107232__CosMx_SMI
Large intestine 1/3 Liver 1/3 Ovary 1/3
Primary cancer 3
CosMx 3 818,673
0/3
 Curated
SPATCH_41107232 · Stereo-seq / Stereo-seq Spatial Transcriptomics
SPATCH_41107232__Stereo_seq
Large intestine 1/3 Liver 1/3 Ovary 1/3
Primary cancer 3
Stereo 3 1,071,400
0/3
 Curated
SPATCH_41107232 · Xenium
SPATCH_41107232__Xenium
Large intestine 1/3 Liver 1/3 Ovary 1/3
Primary cancer 3
Xenium 3 1,087,807
0/3
 Curated
SpinalCord_38513664 · ISS / In Situ Sequencing
SpinalCord_38513664__ISS
Spinal cord 52
Non-cancer disease 52
ISS 52 592,421
52/52
 Curated
SpinalCord_38513664 · Xenium
SpinalCord_38513664__Xenium
Spinal cord 6
Non-cancer disease 4/6 Healthy/control 2/6
Xenium 6 660,801
2/6
 Curated
UlcerativeColitis_38374043 CosMx 1000-plex Run 2 Longitudinal
UlcerativeColitisRun2_38374043__CosMx_SMI
Large intestine 73
Non-cancer disease 50/73 Healthy/control 23/73
CosMx 73 126,368
73/73
 Curated
UlcerativeColitis_38374043 CosMx 960-plex Run 1
UlcerativeColitisRun1_38374043__CosMx_SMI
Large intestine 17
Non-cancer disease 9/17 Healthy/control 8/17
CosMx 17 66,379
17/17
 Curated
Xenium Human Brain Gene Expression Panel showcase
XeniumBrain_10xGenomics__Xenium
Brain 3
Healthy/control 1/3 Non-cancer disease 1/3 Primary cancer 1/3
Xenium 3 110,248
3/3
 Curated
Xenium Human Breast Gene Expression Panel 10x Genomics showcase
XeniumBreast_10xGenomics__Xenium
Breast 6
Primary cancer 6
Xenium 6 3,652,654
0/6
 Curated
Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase
XeniumBreastJanesick_10xGenomics__Xenium
Breast 12
Primary cancer 11/12 Healthy/control 1/12
Xenium 12 3,442,976
0/12
 Curated
Xenium Human Immuno-Oncology Profiling Panel showcase
XeniumImmune_10xGenomics__Xenium
Brain 1/5 Large intestine 1/5 Lung 1/5 Ovary 1/5 Pancreas 1/5
Primary cancer 5
Xenium 5 1,848,679
0/5
 Curated
Xenium Human Lung Gene Expression Panel showcase
XeniumLung_10xGenomics__Xenium
Lung 3
Primary cancer 2/3 Healthy/control 1/3
Xenium 3 1,105,707
0/3
 Curated
Xenium Human Multi-Tissue and Cancer Panel showcase
XeniumMulti_10xGenomics__Xenium
Bone marrow 2/20 Heart 1/20 Kidney 3/20 Liver 2/20 Lung 2/20 Lymphoid tissue 3/20 Musculoskeletal 1/20 Ovary 1/20 Pancreas 3/20 Skin 2/20
Healthy/control 9/20 Primary cancer 9/20 Non-cancer disease 2/20
Xenium 20 5,095,938
6/20
 Curated
cHL_41923627 · CosMx SMI / NanoString SMI
cHL_41923627__CosMx_SMI
Lymphoid tissue 43
Primary cancer 43
CosMx 43 266,199
43/43
 Curated
ASD_42288509 · MERFISH / MERSCOPE
ASD_42288509__MERFISH
Brain 71
Non-cancer disease 71
MERFISH 71 1,515,114
0/71
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