scAtria single-cell spatial atlas resource

Browse

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.
Reset columns
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.
XeniumBreast_10xGenomics__Xenium__Xenium_V1_FFPE_Human_Breast_IDC Xenium Human Breast Gene Expression Panel 10x Genomics showcase Breast Primary cancer Xenium 574,852
MERFISH_500_Vizgen__MERFISH__MERFISHLiverCancerP1 MERFISH 500-plex Vizgen showcase Liver Primary cancer MERFISH 568,355
CosMxWTx_Bruker__CosMx_SMI__CosMxSkinCancerWTx_Bruker Bruker CosMx WTx FFPE showcase Skin Primary cancer CosMx 555,820
GSM8876961_slide_12 CRC_42167227 · CosMx SMI / NanoString SMI CRC_42167227__CosMx_SMI__P12_Res_slide_12 Brain Metastatic cancer CosMx 549,308
HGSC_39179931__CosMx_SMI__HGSC1 HGSC_39179931 · CosMx SMI / NanoString SMI Ovary Primary cancer CosMx 542,559
XeniumLung_10xGenomics__Xenium__Xenium_Preview_Human_Lung_Cancer_With_Add_on_2_FFPE Xenium Human Lung Gene Expression Panel showcase Lung Primary cancer Xenium 531,165
Melanoma_41916292__CyCIF__PT208_6_Post-Pembro Melanoma_41916292 · CyCIF / Cyclic IF Skin Primary cancer CyCIF 513,555
CosMxWTx_Bruker__CosMx_SMI__CosMxColonCancerWTx_Bruker Bruker CosMx WTx FFPE showcase Large intestine Primary cancer CosMx 493,834
MERFISH_500_Vizgen__MERFISH__MERFISHMelanomaP1 MERFISH 500-plex Vizgen showcase Skin Primary cancer MERFISH 468,138
XeniumMulti_10xGenomics__Xenium__Xenium_V1_Human_Kidney_FFPE_Protein_updated Xenium Human Multi-Tissue and Cancer Panel showcase Kidney Primary cancer Xenium 465,534
CosMx1k_Bruker__CosMx_SMI__CosMxLiver1k_Bruker__CancerousLiver Bruker CosMx 1k FFPE showcase Liver Primary cancer CosMx 460,441
Melanoma_41916292__CyCIF__G_GZ7 Melanoma_41916292 · CyCIF / Cyclic IF Skin Primary cancer CyCIF 447,464
Visium_HD_10xGenomics__Visium_HD__Visium_HD_Human_Breast_Cancer_Fixed_Frozen 10x Genomics Visium HD showcase Breast Primary cancer Visium HD 439,422
CosMxWTx_Bruker__CosMx_SMI__CosMxKidneyCancerWTx_Bruker Bruker CosMx WTx FFPE showcase Kidney Primary cancer CosMx 436,787
CosMxWTx_Bruker__CosMx_SMI__CosMxPancreasWTx_Bruker Bruker CosMx WTx FFPE showcase Pancreas Healthy/control CosMx 413,373
SPATCH_41107232__Xenium__SPATCH_Xenium_OV SPATCH_41107232 · Xenium Ovary Primary cancer Xenium 410,193
Xenium5k_10xGenomics__Xenium__Xenium_Prime_Ovarian_Cancer_FFPE_XRrun 10x Genomics Xenium Prime 5K showcase Ovary Primary cancer Xenium 407,124
SPATCH_41107232__Xenium__SPATCH_Xenium_COAD SPATCH_41107232 · Xenium Large intestine Primary cancer Xenium 405,927
SPATCH_41107232__Stereo_seq__SPATCH_Stereo-seq_HCC SPATCH_41107232 · Stereo-seq / Stereo-seq Spatial Transcriptomics Liver Primary cancer Stereo 390,774
XeniumImmune_10xGenomics__Xenium__Xenium_V1_Human_Colorectal_Cancer_Addon_FFPE Xenium Human Immuno-Oncology Profiling Panel showcase Large intestine Primary cancer Xenium 388,175
VisiumHD_p2_WholeSlide__Visium_HD__Visium_HD_6p5mm_Human_Colon_Cancer 10x Genomics Visium HD p2 WholeSlide showcase Large intestine Primary cancer Visium HD 381,174
XeniumBreastJanesick_10xGenomics__Xenium__Human_Breast_Biomarkers_S2_Mid Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase Breast Primary cancer Xenium 380,739
XeniumMulti_10xGenomics__Xenium__Xenium_V1_hLymphNode_nondiseased_section Xenium Human Multi-Tissue and Cancer Panel showcase Lymphoid tissue Healthy/control Xenium 377,985
XeniumBreastJanesick_10xGenomics__Xenium__Human_Breast_Biomarkers_S1_Mid Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase Breast Primary cancer Xenium 375,529
XeniumBreastJanesick_10xGenomics__Xenium__Human_Breast_Biomarkers_S3_Mid Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase Breast Primary cancer Xenium 373,150
11 pcw selected area DevelopingLung_39477961 · PCF / CODEX / PhenoCycler Fusion DevelopingLung_39477961__PCF_CODEX__11w_selectedarea Lung Healthy/control CODEX 373,069
XeniumBreast_10xGenomics__Xenium__Xenium_V1_FFPE_Human_Breast_ILC_With_Addon Xenium Human Breast Gene Expression Panel 10x Genomics showcase Breast Primary cancer Xenium 365,604
SPATCH_41107232__Stereo_seq__SPATCH_Stereo-seq_COAD SPATCH_41107232 · Stereo-seq / Stereo-seq Spatial Transcriptomics Large intestine Primary cancer Stereo 361,260
13 pcw selected area DevelopingLung_39477961 · PCF / CODEX / PhenoCycler Fusion DevelopingLung_39477961__PCF_CODEX__13w_selectedarea Lung Healthy/control CODEX 360,955
XeniumBreastJanesick_10xGenomics__Xenium__Human_Breast_Biomarkers_S2_Bot Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase Breast Primary cancer Xenium 358,519
MERFISH_500_Vizgen__MERFISH__MERFISHOvarianCancerP1 MERFISH 500-plex Vizgen showcase Ovary Primary cancer MERFISH 358,485
XeniumBreast_10xGenomics__Xenium__Xenium_V1_FFPE_Human_Breast_ILC Xenium Human Breast Gene Expression Panel 10x Genomics showcase Breast Primary cancer Xenium 356,746
MERFISH_500_Vizgen__MERFISH__MERFISHLungCancerP1 MERFISH 500-plex Vizgen showcase Lung Primary cancer MERFISH 353,762
XeniumBreastJanesick_10xGenomics__Xenium__Human_Breast_Biomarkers_S4_Mid Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase Breast Primary cancer Xenium 335,709
CosMx1k_Bruker__CosMx_SMI__CosMxLiver1k_Bruker__NormalLiver Bruker CosMx 1k FFPE showcase Liver Healthy/control CosMx 332,877
DLBCL_41120574__CosMx_SMI__F4_1 DLBCL_41120574 · CosMx SMI / NanoString SMI Lymphoid tissue Primary cancer CosMx 332,122
HCC_41723121__CosMx_SMI__Liver_3HT LiverCancer_41723121 HCC cohort · CosMx SMI / NanoString SMI Liver Primary cancer CosMx 330,655
ICC_41723121__CosMx_SMI__Liver_1CB LiverCancer_41723121 iCCA cohort · CosMx SMI / NanoString SMI Liver Primary cancer CosMx 327,199
SPATCH_41107232__PCF_CODEX__SPATCH_PCF_Stereo-seq_OV SPATCH_41107232 · PCF / CODEX / PhenoCycler Fusion Ovary Primary cancer CODEX 325,192
cHL_41923627__MIBI_TOF__R2 cHL_41923627 · MIBI-TOF / Multiplexed Ion Beam Imaging Lymphoid tissue Primary cancer MIBI 323,669
Intestine_39843748__Xenium__GSE280895_timecourse__day6_SI Intestine_39843748 · Xenium Small intestine Healthy/control Xenium 322,464
HCC_41723121__CosMx_SMI__Liver_3HB LiverCancer_41723121 HCC cohort · CosMx SMI / NanoString SMI Liver Primary cancer CosMx 320,670
SPATCH_41107232__Stereo_seq__SPATCH_Stereo-seq_OV SPATCH_41107232 · Stereo-seq / Stereo-seq Spatial Transcriptomics Ovary Primary cancer Stereo 319,366
XeniumBreastJanesick_10xGenomics__Xenium__Human_Breast_Biomarkers_S3_Top Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase Breast Primary cancer Xenium 308,531
Melanoma_41916292__CyCIF__PT42_1_Pre-Enc+Bin Melanoma_41916292 · CyCIF / Cyclic IF Skin Primary cancer CyCIF 302,788
XeniumBreastJanesick_10xGenomics__Xenium__Human_Breast_Biomarkers_S2_Top Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase Breast Healthy/control Xenium 301,854
Visium_HD_10xGenomics__Visium_HD__Visium_HD_Human_Lymph_Node_FFPE 10x Genomics Visium HD showcase Lymphoid tissue Healthy/control Visium HD 300,211
XeniumLung_10xGenomics__Xenium__Xenium_Preview_Human_Non_diseased_Lung_With_Add_on_FFPE Xenium Human Lung Gene Expression Panel showcase Lung Healthy/control Xenium 295,883
HGSC_39179931__CosMx_SMI__HGSC8 HGSC_39179931 · CosMx SMI / NanoString SMI Ovary Primary cancer CosMx 294,699
SPATCH_41107232__CosMx_SMI__SPATCH_CosMx_COAD SPATCH_41107232 · CosMx SMI / NanoString SMI Large intestine Primary cancer CosMx 292,371