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 94 matches · dataset view
Customized columns 7
Dataset table columns Selections persist in the URL and manifest download.
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All records 94 matches
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.
NSCLC_38242124 · IMC / Imaging Mass Cytometry
NSCLC_38242124__IMC
Lung 114/2,070 Lymph node metastasis 1,956/2,070
Primary cancer 2,070
IMC 2,070 5,984,454
2069/2070
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
Melanoma_41916292 · CyCIF / Cyclic IF
Melanoma_41916292__CyCIF
Skin 31
Primary cancer 31
CyCIF 31 3,293,552
21/31
HCC_39327501 · PCF / CODEX / PhenoCycler Fusion
HCC_39327501__PCF_CODEX
Liver 288
Primary cancer 288
CODEX 288 3,231,437
288/288
Intestine_37468586 · PCF / CODEX / PhenoCycler Fusion
Intestine_37468586__PCF_CODEX
Large intestine 27/66 Small intestine 39/66
Healthy/control 66
CODEX 66 2,603,217
64/66
TNBC_38194915 · PCF / CODEX / PhenoCycler Fusion
TNBC_38194915__PCF_CODEX
Breast 27
Primary cancer 27
CODEX 27 2,597,738
16/27
CML_41592325 · PCF / CODEX / PhenoCycler Fusion
CML_41592325__PCF_CODEX
Bone marrow 55
Primary cancer 55
CODEX 55 2,033,725
55/55
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
LUAD_36725934 · IMC / Imaging Mass Cytometry
LUAD_36725934__IMC
Lung 416
Primary cancer 416
IMC 416 1,635,722
415/416
HNSCC_41616773 PCF discovery cohort
HNSCCDiscovery_41616773__PCF_CODEX
Head and neck 189/390 Lymph node metastasis 138/390 Lymphoid tissue 63/390
Primary cancer 189/390 Metastatic cancer 138/390 Healthy/control 63/390
CODEX 390 1,556,569
390/390
NSCLC_40408481 · PCF / CODEX / PhenoCycler Fusion
NSCLC_40408481__PCF_CODEX
Lung 257
Primary cancer 257
CODEX 257 1,450,507
257/257
CastlemanDisease_40593805 · Xenium
CastlemanDisease_40593805__Xenium
Lymphoid tissue 18
Non-cancer disease 18
Xenium 18 1,299,746
12/18
HNSCC_41616773 PCF healthy lymph node cohort
HNSCCHealthyLN_41616773__PCF_CODEX
Lymphoid tissue 51
Healthy/control 51
CODEX 51 1,238,209
50/51
BoneMarrow_38714197 · PCF / CODEX / PhenoCycler Fusion
BoneMarrow_38714197__PCF_CODEX
Bone marrow 32
Healthy/control 27/32 Primary cancer 5/32
CODEX 32 1,214,574
28/32
NormalSkin_41872488 · MERFISH / MERSCOPE
NormalSkin_41872488__MERFISH
Skin 114
Healthy/control 114
MERFISH 114 1,201,886
113/114
DLBCL_41874448 · PCF / CODEX / PhenoCycler Fusion
DLBCL_41874448__PCF_CODEX
Lymphoid tissue 30
Primary cancer 30
CODEX 30 1,172,666
30/30
BrainTumor_36725935 · IMC / Imaging Mass Cytometry
BrainTumor_36725935__IMC
Brain 393
Primary cancer 270/393 Metastatic cancer 123/393
IMC 393 1,163,362
390/393
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
HCC_39304772 · PCF / CODEX / PhenoCycler Fusion
HCC_39304772__PCF_CODEX
Liver 124
Primary cancer 124
CODEX 124 1,065,284
124/124
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
DKD_42056516 · Xenium
DKD_42056516__Xenium
Kidney 16
Non-cancer disease 13/16 Healthy/control 3/16
Xenium 16 951,040
12/16
cHL_41923627 · PCF / CODEX / PhenoCycler Fusion
cHL_41923627__PCF_CODEX
Lymphoid tissue 27
Primary cancer 27
CODEX 27 934,478
27/27
CRC_40189697 · IMC / Imaging Mass Cytometry
CRC_40189697__IMC
Large intestine 170
Primary cancer 170
IMC 170 903,125
170/170
BRCA_31959985 · IMC / Imaging Mass Cytometry
BRCA_31959985__IMC
Breast 376/381 Liver 5/381
Primary cancer 289/381 Healthy/control 92/381
IMC 381 855,668
380/381
Neuroblastoma_41918107 · PCF / CODEX / PhenoCycler Fusion
Neuroblastoma_41918107__PCF_CODEX
Adrenal gland 24
Primary cancer 24
CODEX 24 832,243
24/24
PulmonaryFibrosis_39901013 · Xenium
PulmonaryFibrosis_39901013__Xenium
Lung 45
Non-cancer disease 35/45 Healthy/control 10/45
Xenium 45 790,934
45/45
HNSCC_41616773 PCF validation cohort
HNSCCValidation_41616773__PCF_CODEX
Head and neck 11/34 Lymph node metastasis 10/34 Lymphoid tissue 13/34
Primary cancer 15/34 Metastatic cancer 10/34 Healthy/control 9/34
CODEX 34 745,842
34/34
OSCC_41707652 · IMC / Imaging Mass Cytometry
OSCC_41707652__IMC
Head and neck 92
Primary cancer 92
IMC 92 708,261
92/92
CRC_41986711 · CosMx SMI / NanoString SMI
CRC_41986711__CosMx_SMI
Large intestine 352
Primary cancer 352
CosMx 352 629,446
350/352
SpinalCord_38513664 · ISS / In Situ Sequencing
SpinalCord_38513664__ISS
Spinal cord 52
Non-cancer disease 52
ISS 52 592,421
52/52
BRCA_35122013 · IMC / Imaging Mass Cytometry
BRCA_35122013__IMC
Breast 548
Primary cancer 548
IMC 548 479,844
547/548
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
Neocortex_39779846 · MERFISH / MERSCOPE
Neocortex_39779846__MERFISH
Brain 6
Healthy/control 6
MERFISH 6 404,030
5/6
HCC_39965889 · PCF / CODEX / PhenoCycler Fusion
HCC_39965889__PCF_CODEX
Liver 31
Primary cancer 31
CODEX 31 387,155
31/31
Melanoma_35363543 · IMC / Imaging Mass Cytometry
Melanoma_35363543__IMC
Bone marrow 1/72 Brain 4/72 Large intestine 5/72 Lymph node metastasis 20/72 Skin 42/72
Primary cancer 31/72 Metastatic cancer 29/72 Healthy/control 12/72
IMC 72 272,135
72/72
cHL_41923627 · CosMx SMI / NanoString SMI
cHL_41923627__CosMx_SMI
Lymphoid tissue 43
Primary cancer 43
CosMx 43 266,199
43/43
CRC_32763154 · PCF / CODEX / PhenoCycler Fusion
CRC_32763154__PCF_CODEX
Large intestine 140
Primary cancer 140
CODEX 140 258,385
140/140
DLBCL_41874448 · CosMx SMI / NanoString SMI
DLBCL_41874448__CosMx_SMI
Lymphoid tissue 56
Primary cancer 56
CosMx 56 182,646
56/56
CutaneousLeishmaniasis_40371647 · CosMx SMI / NanoString SMI
CutaneousLeishmaniasis_40371647__CosMx_SMI
Skin 4
Non-cancer disease 4
CosMx 4 130,801
4/4
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
10x Genomics Visium HD p2 TMA showcase
VisiumHD_p2_TMA__Visium_HD
Breast 36
Primary cancer 36
Visium HD 36 117,494
36/36
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
PDAC_40269162 · CosMx SMI / NanoString SMI
PDAC_40269162__CosMx_SMI
Pancreas 90
Primary cancer 90
CosMx 90 82,348
84/90
BRCA_35063072 · MIBI-TOF / Multiplexed Ion Beam Imaging
BRCA_35063072__MIBI_TOF
Breast 79
Primary cancer 70/79 Healthy/control 9/79
MIBI 79 69,672
79/79
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
HCC_39455893 · IMC / Imaging Mass Cytometry
HCC_39455893__IMC
Liver 38
Primary cancer 38
IMC 38 61,393
38/38
Melanoma_40148341 · CosMx SMI / NanoString SMI
Melanoma_40148341__CosMx_SMI
Skin 25
Primary cancer 25
CosMx 25 56,761
25/25
IBD_42049732 · CosMx SMI / NanoString SMI
IBD_42049732__CosMx_SMI
Large intestine 34
Non-cancer disease 34
CosMx 34 43,034
34/34
SCN_41720090 · Visium HD
SCN_41720090__Visium_HD
Brain 1
Healthy/control 1
Visium HD 1 16,123
1/1
SCN_41720090 · MERFISH / MERSCOPE
SCN_41720090__MERFISH
Brain 1
Healthy/control 1
MERFISH 1 6,953
1/1