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.
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View mode ?Cards are for quick scanning. Tables are denser and better for comparison, sorting, and column customization.
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494 Samples
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.
Examples Study ID HNSCC_41616773 Modality Spatial transcriptomics Technique Xenium Organ breast Disease state primary cancer Disease detail breast cancer
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Organ: Brain × 494 matches 417 curated 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. Curation ?Curated records have standardized ontology labels and normalized metadata. Source records are ingested but not fully standardized yet.
Melanoma_35363543__IMC__12RD Melanoma_35363543 · IMC / Imaging Mass Cytometry Brain Metastatic cancer IMC 2,796 T1T2T3T1T2T3T1T2T3 Curated
Melanoma_35363543__IMC__39RD Melanoma_35363543 · IMC / Imaging Mass Cytometry Brain Metastatic cancer IMC 2,391 T1T2T3T1T2T3T1T2T3 Curated
MERFISH_960_Vizgen__MERFISH__MERFISH960HuBrainS3_R1 MERFISH 960-plex Vizgen showcase Brain Healthy/control MERFISH 69,931 T1T2T3T1T2T3T1T2T3 Curated
MERFISH_960_Vizgen__MERFISH__MERFISH960HuBrainS3_R2 MERFISH 960-plex Vizgen showcase Brain Non-cancer disease MERFISH 186,623 Curated
MERFISH_960_Vizgen__MERFISH__MERFISH960HuBrainSF_R0 MERFISH 960-plex Vizgen showcase Brain Non-cancer disease MERFISH 137,627 Curated
ARKFrozen-62-PFC Neocortex_39779846 · MERFISH / MERSCOPE Neocortex_39779846__MERFISH__ARKFrozen-62-PFC Brain Healthy/control MERFISH 51,074 T1T2T3T1T2T3T1T2T3 Curated
ARKFrozen-65-V1 Neocortex_39779846 · MERFISH / MERSCOPE Neocortex_39779846__MERFISH__ARKFrozen-65-V1 Brain Healthy/control MERFISH 169,905 Curated
NIH-4365-BA10 Neocortex_39779846 · MERFISH / MERSCOPE Neocortex_39779846__MERFISH__NIH-4365-BA10 Brain Healthy/control MERFISH 52,483 T1T2T3T1T2T3T1T2T3 Curated
NIH-4392-BA17 Neocortex_39779846 · MERFISH / MERSCOPE Neocortex_39779846__MERFISH__NIH-4392-BA17 Brain Healthy/control MERFISH 26,593 T1T2T3T1T2T3T1T2T3 Curated
NIH-5900-BA17 Neocortex_39779846 · MERFISH / MERSCOPE Neocortex_39779846__MERFISH__NIH-5900-BA17 Brain Healthy/control MERFISH 56,343 T1T2T3T1T2T3T1T2T3 Curated
UCSF2018-003-MFG Neocortex_39779846 · MERFISH / MERSCOPE Neocortex_39779846__MERFISH__UCSF2018-003-MFG Brain Healthy/control MERFISH 47,632 T1T2T3T1T2T3T1T2T3 Curated
SCN_41720090__MERFISH__202408121157_humanbrainAP1615_VMSC03601_region_0 SCN_41720090 · MERFISH / MERSCOPE Brain Healthy/control MERFISH 6,953 T1T2T3T1T2T3T1T2T3 Curated
SCN_41720090__Visium_HD__slice46_HD_expand_cell_4_10genes SCN_41720090 · Visium HD Brain Healthy/control Visium HD 16,123 T1T2T3T1T2T3T1T2T3 Curated
XeniumBrain_10xGenomics__Xenium__Xenium_V1_FFPE_Human_Brain_Alzheimers_With_Addon Xenium Human Brain Gene Expression Panel showcase Brain Healthy/control Xenium 44,955 T1T2T3T1T2T3T1T2T3 Curated
XeniumBrain_10xGenomics__Xenium__Xenium_V1_FFPE_Human_Brain_Glioblastoma_With_Addon Xenium Human Brain Gene Expression Panel showcase Brain Primary cancer Xenium 40,887 T1T2T3T1T2T3T1T2T3 Curated
XeniumBrain_10xGenomics__Xenium__Xenium_V1_FFPE_Human_Brain_Healthy_With_Addon Xenium Human Brain Gene Expression Panel showcase Brain Non-cancer disease Xenium 24,406 T1T2T3T1T2T3T1T2T3 Curated
XeniumImmune_10xGenomics__Xenium__Xenium_V1_Human_Brain_GBM_FFPE Xenium Human Immuno-Oncology Profiling Panel showcase Brain Primary cancer Xenium 816,769 Curated
GSM5910280_Panel1_CW60220F-1_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910280_Panel1_CW60220F-1_i Brain Non-cancer disease MERFISH 38,263 Source
GSM5910281_Panel1_CW60230E-1_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910281_Panel1_CW60230E-1_i Brain Non-cancer disease MERFISH 33,845 Source
GSM5910282_Panel1_CW20012E-1_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910282_Panel1_CW20012E-1_i Brain Non-cancer disease MERFISH 23,390 Source
GSM5910283_Panel1_CW60040F-1_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910283_Panel1_CW60040F-1_i Brain Non-cancer disease MERFISH 16,178 Source
GSM5910284_Panel1_CW20053A-1_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910284_Panel1_CW20053A-1_i Brain Non-cancer disease MERFISH 34,305 Source
GSM5910285_Panel1_CW20069F-1_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910285_Panel1_CW20069F-1_i Brain Non-cancer disease MERFISH 27,708 Source
GSM5910286_Panel1_CW60218E-1_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910286_Panel1_CW60218E-1_i Brain Non-cancer disease MERFISH 38,964 Source
GSM5910287_Panel1_CW60219E-1_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910287_Panel1_CW60219E-1_i Brain Non-cancer disease MERFISH 14,837 Source
GSM5910288_Panel1_CW60220F-2_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910288_Panel1_CW60220F-2_i Brain Non-cancer disease MERFISH 22,461 Source
GSM5910289_Panel1_CW60230E-2_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910289_Panel1_CW60230E-2_i Brain Non-cancer disease MERFISH 6,717 Source
GSM5910290_Panel1_CW60218E-2_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910290_Panel1_CW60218E-2_i Brain Non-cancer disease MERFISH 31,875 Source
GSM5910291_Panel1_CW60040F-2_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910291_Panel1_CW60040F-2_i Brain Non-cancer disease MERFISH 49,596 Source
GSM5910292_Panel2_CW60220F-3_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910292_Panel2_CW60220F-3_i Brain Non-cancer disease MERFISH 7,270 Source
GSM5910293_Panel2_CW60230E-4_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910293_Panel2_CW60230E-4_i Brain Non-cancer disease MERFISH 12,972 Source
GSM5910294_Panel2_CW20012E-2_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910294_Panel2_CW20012E-2_i Brain Non-cancer disease MERFISH 20,583 Source
GSM5910295_Panel2_CW60219E-2_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910295_Panel2_CW60219E-2_i Brain Non-cancer disease MERFISH 34,616 Source
GSM5910296_Panel2_CW60040F-3_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910296_Panel2_CW60040F-3_i Brain Non-cancer disease MERFISH 21,116 Source
GSM5910297_Panel2_CW20053A-2_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910297_Panel2_CW20053A-2_i Brain Non-cancer disease MERFISH 15,542 Source
GSM5910298_Panel2_CW20047D-3_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910298_Panel2_CW20047D-3_i Brain Non-cancer disease MERFISH 15,543 Source
GSM5910299_Panel2_CW60040F-4_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910299_Panel2_CW60040F-4_i Brain Non-cancer disease MERFISH 21,137 Source
GSM5910300_Panel3_CW60040F-5_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910300_Panel3_CW60040F-5_i Brain Non-cancer disease MERFISH 8,181 Source
GSM5910301_Panel3_CW60219E-3_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910301_Panel3_CW60219E-3_i Brain Non-cancer disease MERFISH 34,963 Source
GSM5910302_Panel3_CW20012E-2_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910302_Panel3_CW20012E-2_i Brain Non-cancer disease MERFISH 13,636 Source
GSM5910303_Panel3_CW20041A-2_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910303_Panel3_CW20041A-2_i Brain Non-cancer disease MERFISH 13,004 Source
GSM5910304_Panel3_CW20047D-4_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910304_Panel3_CW20047D-4_i Brain Non-cancer disease MERFISH 7,955 Source
GSM5910305_Panel3_CW60219E-3_ii ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910305_Panel3_CW60219E-3_ii Brain Non-cancer disease MERFISH 34,178 Source
GSM5910306_Panel3_CW60230E-4_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910306_Panel3_CW60230E-4_i Brain Non-cancer disease MERFISH 34,839 Source
GSM5910307_Panel3_CW20012E-2_ii ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910307_Panel3_CW20012E-2_ii Brain Non-cancer disease MERFISH 21,940 Source
GSM5910308_Panel3_CW20053A-2_ii ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910308_Panel3_CW20053A-2_ii Brain Non-cancer disease MERFISH 16,419 Source
GSM5910309_Panel3_CW20053A-2_ii ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910309_Panel3_CW20053A-2_ii Brain Non-cancer disease MERFISH 14,805 Source
GSM5910310_Panel3_CW60219E-4_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910310_Panel3_CW60219E-4_i Brain Non-cancer disease MERFISH 31,932 Source
GSM5910311_Panel3_CW60220F-4_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910311_Panel3_CW60220F-4_i Brain Non-cancer disease MERFISH 19,819 Source
GSM5910312_Panel3_CW20047D-3_i ASD_42288509 · MERFISH / MERSCOPE ASD_42288509__MERFISH__GSM5910312_Panel3_CW20047D-3_i Brain Non-cancer disease MERFISH 18,343 Source