scAtria single-cell spatial atlas resource

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Dataset Sample
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67 Datasets
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Examples Study ID HNSCC_41616773 Modality Spatial transcriptomics Technique Xenium Organ breast Disease state primary cancer Disease detail breast cancer
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Disease state: Primary cancer × 67 matches 59 curated
Dataset Organs ?For mixed datasets, fractions show sample counts per organ. Disease state Technique Samples Cells Spatial module Curation
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
33/36
 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
0/3
 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
0/24
 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
B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion
B-NHL_38379051__PCF_CODEX
Lymphoid tissue 35
Primary cancer 35
CODEX 35 5,690,284
0/35
 Curated
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
373/381
 Curated
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
 Curated
BRCA_35122013 · IMC / Imaging Mass Cytometry
BRCA_35122013__IMC
Breast 548
Primary cancer 548
IMC 548 479,844
547/548
 Curated
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
11/32
 Curated
BrainTumor_36725935 · IMC / Imaging Mass Cytometry
BrainTumor_36725935__IMC
Brain 393
Primary cancer 270/393 Metastatic cancer 123/393
IMC 393 1,163,362
377/393
 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 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
0/9
 Curated
CML_41592325 · PCF / CODEX / PhenoCycler Fusion
CML_41592325__PCF_CODEX
Bone marrow 55
Primary cancer 55
CODEX 55 2,033,725
0/55
 Curated
CRC_32763154 · PCF / CODEX / PhenoCycler Fusion
CRC_32763154__PCF_CODEX
Large intestine 140
Primary cancer 140
CODEX 140 258,385
140/140
 Curated
CRC_40189697 · IMC / Imaging Mass Cytometry
CRC_40189697__IMC
Large intestine 170
Primary cancer 170
IMC 170 903,125
71/170
 Curated
CRC_41986711 · CosMx SMI / NanoString SMI
CRC_41986711__CosMx_SMI
Large intestine 352
Primary cancer 352
CosMx 352 629,446
350/352
 Curated
CervicalCancer_CmTSA_41807362
CervicalCancer_CmTSA_41807362__CmTSA
Uterus/Cervix 2
Primary cancer 2
CmTSA 2 1,564,537
0/2
 Curated
DLBCL_41874448 · CosMx SMI / NanoString SMI
DLBCL_41874448__CosMx_SMI
Lymphoid tissue 56
Primary cancer 56
CosMx 56 182,646
56/56
 Curated
DLBCL_41874448 · PCF / CODEX / PhenoCycler Fusion
DLBCL_41874448__PCF_CODEX
Lymphoid tissue 30
Primary cancer 30
CODEX 30 1,172,666
0/30
 Curated
HCC_39304772 · PCF / CODEX / PhenoCycler Fusion
HCC_39304772__PCF_CODEX
Liver 124
Primary cancer 124
CODEX 124 1,065,284
38/124
 Curated
HCC_39327501 · PCF / CODEX / PhenoCycler Fusion
HCC_39327501__PCF_CODEX
Liver 288
Primary cancer 288
CODEX 288 3,231,437
3/288
 Curated
HCC_39455893 · IMC / Imaging Mass Cytometry
HCC_39455893__IMC
Liver 38
Primary cancer 38
IMC 38 61,393
37/38
 Curated
HCC_39965889 · PCF / CODEX / PhenoCycler Fusion
HCC_39965889__PCF_CODEX
Liver 31
Primary cancer 31
CODEX 31 387,155
10/31
 Curated
HGSC_39179931 · CosMx SMI / NanoString SMI
HGSC_39179931__CosMx_SMI
Ovary 166
Primary cancer 166
CosMx 166 1,724,825
122/166
 Curated
HGSC_39179931 · MERFISH / MERSCOPE
HGSC_39179931__MERFISH
Ovary 4
Primary cancer 4
MERFISH 4 425,578
0/4
 Curated
HGSC_39179931 · Xenium
HGSC_39179931__Xenium
Ovary 32
Primary cancer 32
Xenium 32 447,874
3/32
 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
49/137
 Curated
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
293/390
 Curated
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
2/34
 Curated
LUAD_36725934 · IMC / Imaging Mass Cytometry
LUAD_36725934__IMC
Lung 416
Primary cancer 416
IMC 416 1,635,722
386/416
 Curated
LiverCancer_41723121 HCC cohort · CosMx SMI / NanoString SMI
HCC_41723121__CosMx_SMI
Liver 9
Primary cancer 9
CosMx 9 1,446,124
0/9
 Curated
LiverCancer_41723121 iCCA cohort · CosMx SMI / NanoString SMI
ICC_41723121__CosMx_SMI
Liver 6
Primary cancer 6
CosMx 6 901,465
0/6
 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
0/18
 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
0/6
 Curated
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
 Curated
Melanoma_40148341 · CosMx SMI / NanoString SMI
Melanoma_40148341__CosMx_SMI
Skin 25
Primary cancer 25
CosMx 25 56,761
24/25
 Curated
Melanoma_41916292 · CyCIF / Cyclic IF
Melanoma_41916292__CyCIF
Skin 31
Primary cancer 31
CyCIF 31 3,293,552
1/31
 Curated
NSCLC_38242124 · IMC / Imaging Mass Cytometry
NSCLC_38242124__IMC
Lung 2,070
Primary cancer 2,070
IMC 2,070 5,984,454
2025/2070
 Curated
NSCLC_40408481 · PCF / CODEX / PhenoCycler Fusion
NSCLC_40408481__PCF_CODEX
Lung 257
Primary cancer 257
CODEX 257 1,450,507
141/257
 Curated
Neuroblastoma_41918107 · PCF / CODEX / PhenoCycler Fusion
Neuroblastoma_41918107__PCF_CODEX
Adrenal gland 24
Primary cancer 24
CODEX 24 832,243
0/24
 Curated
OSCC_41707652 · IMC / Imaging Mass Cytometry
OSCC_41707652__IMC
Head and neck 92
Primary cancer 92
IMC 92 708,261
6/92
 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
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 · PCF / CODEX / PhenoCycler Fusion
SPATCH_41107232__PCF_CODEX
Large intestine 3/9 Liver 3/9 Ovary 3/9
Primary cancer 9
CODEX 9 1,970,702
0/9
 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
TNBC_38194915 · PCF / CODEX / PhenoCycler Fusion
TNBC_38194915__PCF_CODEX
Breast 27
Primary cancer 27
CODEX 27 2,597,738
0/27
 Curated