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 7,721 matches · sample view
Customized columns 6
Sample table columns Selections persist in the URL and manifest download.
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All records 7,721 matches Download sample CSV
Sample Organ Disease state ?Broad public sample state used for filtering and comparison. Technique Cells ?Number of individually resolved single-cell observations included for the record. Spatial module ?D, I, and T indicate Domains, Interaction, and Topology outputs. Tier badges show ready ontology levels when detailed availability is available.
MERFISH_500_Vizgen__MERFISH__MERFISHMelanomaP2 MERFISH 500-plex Vizgen showcase Skin Primary cancer MERFISH 207,869
Liver_41986723__MERFISH__M8 Liver_41986723 · MERFISH / MERSCOPE Liver Healthy/control MERFISH 207,498
B-NHL_38379051__PCF_CODEX__191_2reg001 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 206,365
XeniumMulti_10xGenomics__Xenium__Xenium_V1_Human_Ovary_Cancer_FF Xenium Human Multi-Tissue and Cancer Panel showcase Ovary Primary cancer Xenium 205,082
B-NHL_38379051__PCF_CODEX__191_5reg002 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 203,531
XeniumBreastJanesick_10xGenomics__Xenium__Human_Breast_Biomarkers_S4_Bot Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase Breast Primary cancer Xenium 201,955
Xenium5k_10xGenomics__Xenium__Xenium_Prime_Human_Ovary_Cancer_FF 10x Genomics Xenium Prime 5K showcase Ovary Primary cancer Xenium 200,900
Visium_HD_10xGenomics__Visium_HD__Visium_HD_3prime_Human_Ovarian_Cancer 10x Genomics Visium HD showcase Ovary Primary cancer Visium HD 200,764
12 pcw selected area DevelopingLung_39477961 · PCF / CODEX / PhenoCycler Fusion DevelopingLung_39477961__PCF_CODEX__12w_selectedarea Lung Healthy/control CODEX 200,625
TNBC_38194915__PCF_CODEX__210201_Breast_Cassette1_reg1_v5 TNBC_38194915 · PCF / CODEX / PhenoCycler Fusion Breast Primary cancer CODEX 200,217
B-NHL_38379051__PCF_CODEX__191_2reg004 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 200,175
Intestine_39843748__Xenium__GSE280895_timecourse__day8_SI_r2 Intestine_39843748 · Xenium Small intestine Healthy/control Xenium 198,887
DKD_42056516__CosMx_SMI__HK3039 DKD_42056516 · CosMx SMI / NanoString SMI Kidney Healthy/control CosMx 196,590
Xenium5k_10xGenomics__Xenium__Xenium_Prime_Human_Prostate_FFPE 10x Genomics Xenium Prime 5K showcase Prostate Primary cancer Xenium 193,000
XeniumBreastJanesick_10xGenomics__Xenium__Human_Breast_Biomarkers_S4_Top Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase Breast Primary cancer Xenium 192,898
Intestine_39843748__Xenium__GSE280895_uninfected__segmentation_SI2 Intestine_39843748 · Xenium Small intestine Healthy/control Xenium 191,024
XeniumMulti_10xGenomics__Xenium__Xenium_V1_hPancreas_Cancer_Add_on_FFPE Xenium Human Multi-Tissue and Cancer Panel showcase Pancreas Primary cancer Xenium 190,965
CosMx6k_Bruker__CosMx_SMI__CosMxFrontalCortex6k_Bruker Bruker CosMx 6k FFPE showcase Brain Healthy/control CosMx 188,686
DKD_42056516__CosMx_SMI__HK2844 DKD_42056516 · CosMx SMI / NanoString SMI Kidney Non-cancer disease CosMx 186,643
MERFISH_960_Vizgen__MERFISH__MERFISH960HuBrainS3_R2 MERFISH 960-plex Vizgen showcase Brain Non-cancer disease MERFISH 186,623
Visium_HD_10xGenomics__Visium_HD__Visium_HD_Human_Ovarian_Cancer_FF 10x Genomics Visium HD showcase Ovary Primary cancer Visium HD 183,450
Visium_HD_10xGenomics__Visium_HD__Visium_HD_Human_Ovarian_Cancer_FF_Min_Depth 10x Genomics Visium HD showcase Ovary Primary cancer Visium HD 183,449
B-NHL_38379051__PCF_CODEX__191_3reg003 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 181,205
B-NHL_38379051__PCF_CODEX__191_2reg007 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 181,135
DKD_42056516__CosMx_SMI__HK3565 DKD_42056516 · CosMx SMI / NanoString SMI Kidney Healthy/control CosMx 179,861
B-NHL_38379051__PCF_CODEX__191_5reg004 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 179,598
B-NHL_38379051__PCF_CODEX__191_2reg002 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 176,664
ICC_41723121__CosMx_SMI__Liver_3CB LiverCancer_41723121 iCCA cohort · CosMx SMI / NanoString SMI Liver Primary cancer CosMx 174,833
B-NHL_38379051__PCF_CODEX__191_2reg003 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 174,640
B-NHL_38379051__PCF_CODEX__191_3reg005 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 174,321
B-NHL_38379051__PCF_CODEX__191_5reg006 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 174,302
TNBC_38194915__PCF_CODEX__210113_Breast_Cassette11_reg1_v5 TNBC_38194915 · PCF / CODEX / PhenoCycler Fusion Breast Primary cancer CODEX 173,460
B-NHL_38379051__PCF_CODEX__191_1reg002 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 172,066
TNBC_38194915__PCF_CODEX__210208_Breast_Cassette6_reg2_v5 TNBC_38194915 · PCF / CODEX / PhenoCycler Fusion Breast Primary cancer CODEX 171,606
DKD_42056516__Xenium__HK3106 DKD_42056516 · Xenium Kidney Healthy/control Xenium 171,526
GSM8876957_slide_8 CRC_42167227 · CosMx SMI / NanoString SMI CRC_42167227__CosMx_SMI__P4_Res_slide_8 Brain Metastatic cancer CosMx 171,124
Melanoma_41916292__CyCIF__PT35_3_On-Dab+Tra_Pre-Ipi Melanoma_41916292 · CyCIF / Cyclic IF Skin Primary cancer CyCIF 170,152
Atera_10xGenomics__Atera__WTA_Preview_FFPE_Breast_Cancer 10x Genomics Atera showcase Breast Primary cancer Atera 170,057
ARKFrozen-65-V1 Neocortex_39779846 · MERFISH / MERSCOPE Neocortex_39779846__MERFISH__ARKFrozen-65-V1 Brain Healthy/control MERFISH 169,905
TNBC_38194915__PCF_CODEX__210129_Breast_Cassette4_reg1_v5 TNBC_38194915 · PCF / CODEX / PhenoCycler Fusion Breast Primary cancer CODEX 169,656
DLBCL_41120574__CosMx_SMI__F6_3 DLBCL_41120574 · CosMx SMI / NanoString SMI Lymphoid tissue Primary cancer CosMx 167,868
B-NHL_38379051__PCF_CODEX__191_4reg002 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 167,286
B-NHL_38379051__PCF_CODEX__191_5reg005 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 165,172
SPATCH_41107232__PCF_CODEX__SPATCH_PCF_Stereo-seq_COAD SPATCH_41107232 · PCF / CODEX / PhenoCycler Fusion Large intestine Primary cancer CODEX 165,142
Visium_HD_10xGenomics__Visium_HD__Visium_HD_Human_Lung_Cancer_HD_Only_Experiment2 10x Genomics Visium HD showcase Lung Primary cancer Visium HD 165,128
B-NHL_38379051__PCF_CODEX__191_4reg007 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 164,496
TNBC_38194915__PCF_CODEX__210205_Breast_Cassette2_reg1_v5 TNBC_38194915 · PCF / CODEX / PhenoCycler Fusion Breast Primary cancer CODEX 164,096
B-NHL_38379051__PCF_CODEX__191_3reg006 B-NHL_38379051 · PCF / CODEX / PhenoCycler Fusion Lymphoid tissue Primary cancer CODEX 162,943
XeniumMulti_10xGenomics__Xenium__Xenium_V1_hLiver_cancer_section_FFPE Xenium Human Multi-Tissue and Cancer Panel showcase Liver Primary cancer Xenium 162,628
XeniumMulti_10xGenomics__Xenium__Xenium_V1_humanLung_Cancer_FFPE Xenium Human Multi-Tissue and Cancer Panel showcase Lung Primary cancer Xenium 162,254