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.
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Dataset table columns
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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
LUAD_36725934 · IMC / Imaging Mass Cytometry
LUAD_36725934__IMC
Lung 416
Primary cancer 416
IMC 416 1,635,722
415/416
NSCLC_40408481 · PCF / CODEX / PhenoCycler Fusion
NSCLC_40408481__PCF_CODEX
Lung 257
Primary cancer 257
CODEX 257 1,450,507
257/257
PulmonaryFibrosis_39901013 · Xenium
PulmonaryFibrosis_39901013__Xenium
Lung 45
Non-cancer disease 35/45 Healthy/control 10/45
Xenium 45 790,934
45/45
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
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
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
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
CRC_42167227 · CosMx SMI / NanoString SMI
CRC_42167227__CosMx_SMI
Brain 2/45 Liver 30/45 Lung 10/45 Peritoneum 3/45
Metastatic cancer 45
CosMx 45 1,874,376
0/45
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
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
DevelopingLung_39477961 · PCF / CODEX / PhenoCycler Fusion
DevelopingLung_39477961__PCF_CODEX
Lung 5
Healthy/control 5
CODEX 5 971,112
0/5
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
NSCLC_40220761 · CosMx SMI / NanoString SMI
NSCLC_40220761__CosMx_SMI
Lung 6
Primary cancer 6
CosMx 6 350,199
0/6