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.
HCC_39327501 · PCF / CODEX / PhenoCycler Fusion
HCC_39327501__PCF_CODEX
Liver 288
Primary cancer 288
CODEX 288 3,231,437
288/288
HCC_39304772 · PCF / CODEX / PhenoCycler Fusion
HCC_39304772__PCF_CODEX
Liver 124
Primary cancer 124
CODEX 124 1,065,284
124/124
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
HCC_39965889 · PCF / CODEX / PhenoCycler Fusion
HCC_39965889__PCF_CODEX
Liver 31
Primary cancer 31
CODEX 31 387,155
31/31
HCC_39455893 · IMC / Imaging Mass Cytometry
HCC_39455893__IMC
Liver 38
Primary cancer 38
IMC 38 61,393
38/38
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
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
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
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
LiverCancer_41723121 HCC cohort · CosMx SMI / NanoString SMI
HCC_41723121__CosMx_SMI
Liver 9
Primary cancer 9
CosMx 9 1,446,124
4/9
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
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
LiverCancer_41723121 iCCA cohort · CosMx SMI / NanoString SMI
ICC_41723121__CosMx_SMI
Liver 6
Primary cancer 6
CosMx 6 901,465
3/6
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
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
Liver_41986723 · MERFISH / MERSCOPE
Liver_41986723__MERFISH
Liver 2
Healthy/control 2
MERFISH 2 310,412
0/2