Datasets
94
80 curated
Cross-study table
Studies ordered by reference
| Study | Reference | Datasets | Curated | Samples | Cells |
|---|---|---|---|---|---|
|
10x Genomics Atera showcase
Atera_10xGenomics
|
10x Genomics Atera official dataset
10x Genomics
|
1 | 1 | 2 | 887,633 |
|
10x Genomics Visium HD p2 TissueArray showcase
VisiumHD_p2_TissueArray
|
10x Genomics Visium HD protocol 2.0 TissueArray official dataset
10x Genomics
|
1 | 1 | 3 | 506,235 |
|
10x Genomics Visium HD p2 TMA showcase
VisiumHD_p2_TMA
|
10x Genomics Visium HD protocol 2.0 TMA official dataset
10x Genomics
|
1 | 1 | 36 | 117,494 |
|
10x Genomics Visium HD p2 WholeSlide showcase
VisiumHD_p2_WholeSlide
|
10x Genomics Visium HD protocol 2.0 WholeSlide official dataset
10x Genomics
|
1 | 1 | 3 | 1,729,339 |
|
Xenium Human Brain Gene Expression Panel showcase
XeniumBrain_10xGenomics
|
10x Genomics Xenium Human Brain official dataset
10x Genomics
|
1 | 1 | 3 | 110,248 |
|
Xenium Human Breast Gene Expression Panel 10x Genomics showcase
XeniumBreast_10xGenomics
|
10x Genomics Xenium Human Breast official dataset
10x Genomics
|
1 | 1 | 6 | 3,652,654 |
|
Xenium Human Immuno-Oncology Profiling Panel showcase
XeniumImmune_10xGenomics
|
10x Genomics Xenium Human Immuno-Oncology official dataset
10x Genomics
|
1 | 1 | 5 | 1,848,679 |
|
Xenium Human Lung Gene Expression Panel showcase
XeniumLung_10xGenomics
|
10x Genomics Xenium Human Lung official dataset
10x Genomics
|
1 | 1 | 3 | 1,105,707 |
|
Xenium Human Multi-Tissue and Cancer Panel showcase
XeniumMulti_10xGenomics
|
10x Genomics Xenium Human Multi-Tissue and Cancer official dataset
10x Genomics
|
1 | 1 | 20 | 5,095,938 |
|
10x Genomics Xenium Prime 5K showcase
Xenium5k_10xGenomics
|
10x Genomics Xenium Prime 5K official dataset
10x Genomics
|
1 | 1 | 9 | 4,598,042 |
| PDAC_41916312 |
A convergent uPAR-positive tumor ecosystem creates broad vulnerability to CAR T cell therapy.
Cell · 2026
|
1 | 0 | 1 | 77,695 |
| Melanoma_41916292 |
A longitudinal, multi-omic atlas reveals the emergence of a spatially organized immunosuppressive ecosystem in resistant melanoma.
Cell Reports Medicine · 2026
|
1 | 1 | 31 | 3,293,552 |
| MIBC_42126225 |
A Spatial Atlas of Muscle-Invasive Bladder Cancer Reveals Lineage-Specific Vulnerabilities and Immune Architecture.
Cancer Discovery · 2026
|
1 | 0 | 5 | 131,875 |
| Liver_41986723 |
A spatial atlas of the healthy human liver from live donors.
Nature · 2026
|
1 | 0 | 2 | 310,412 |
| Intestine_37468586 |
A spatially resolved single-cell genomic atlas of the adult human intestine.
Nature · 2023
|
1 | 1 | 66 | 2,603,217 |
|
Xenium Human Breast Gene Expression Panel bioRxiv biomarker showcase
XeniumBreastJanesick_10xGenomics
|
Biomarker Quantification in Breast Cancer using Xenium In Situ
bioRxiv · 2025
|
1 | 1 | 12 | 3,442,976 |
|
Bruker CosMx 1k FFPE showcase
CosMx1k_Bruker
|
Bruker CosMx 1k FFPE official dataset
Bruker Spatial Biology
|
1 | 1 | 2 | 793,318 |
|
Bruker CosMx 6k FFPE showcase
CosMx6k_Bruker
|
Bruker CosMx 6k FFPE official dataset
Bruker Spatial Biology
|
1 | 1 | 2 | 2,041,632 |
|
Bruker CosMx 64-protein FFPE showcase
CosMx64_Bruker
|
Bruker CosMx 64-protein FFPE official dataset
Bruker Spatial Biology
|
1 | 1 | 2 | 1,398,757 |
|
Bruker CosMx WTx FFPE showcase
CosMxWTx_Bruker
|
Bruker CosMx WTx FFPE official dataset
Bruker Spatial Biology
|
1 | 1 | 9 | 2,878,028 |
| NSCLC_38242124 |
Cancer-associated fibroblast phenotypes are associated with patient outcome in non-small cell lung cancer.
Cancer Cell · 2024
|
1 | 1 | 2,070 | 5,984,454 |
| SpinalCord_38513664 |
Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology.
Cell · 2024
|
2 | 2 | 58 | 1,253,222 |
| NSCLC_40220761 |
Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment.
Cell systems · 2025
|
1 | 0 | 6 | 350,199 |
| CRC_42167227 |
Concurrent genetic and non-genetic resistance mechanisms to KRAS inhibition in colorectal cancer.
Cancer Cell · 2026
|
1 | 0 | 14 | 1,901,559 |
| CRC_32763154 |
Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front.
Cell · 2020
|
1 | 1 | 140 | 258,385 |
| Oral_41663813 |
Distinct spatial organization governs oral mucosal immunity.
Nature Immunology · 2026
|
1 | 0 | 44 | 710,477 |
| CRC_41986711 |
Emergence of oncofetal plasticity is ubiquitous in early colorectal cancers.
Nature · 2026
|
1 | 1 | 352 | 629,446 |
| cHL_41923627 |
Epstein-Barr virus orchestrates spatial reorganization and immunomodulation in the classic Hodgkin lymphoma tumor microenvironment.
Cell Reports Medicine · 2026
|
3 | 3 | 79 | 2,609,887 |
|
10x Genomics Visium HD showcase
Visium_HD_10xGenomics
|
High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer.
Nature Genetics · 2025
|
1 | 1 | 24 | 5,379,712 |
| CML_41592325 |
High-dimensional spatiotemporal single-cell atlas and 3D imaging of bone marrow microenvironment during CML progression
Blood · 2025
|
1 | 1 | 55 | 2,033,725 |
| DevelopingLung_39477961 |
High-parametric protein maps reveal the spatial organization in early-developing human lung.
Nature Communications · 2024
|
1 | 0 | 5 | 971,112 |
| CutaneousLeishmaniasis_40371647 |
IL-32-producing CD8+ memory T cells define immunoregulatory niches in human cutaneous leishmaniasis.
The Journal of clinical investigation · 2025
|
1 | 1 | 4 | 130,801 |
| BRCA_35122013 |
Imaging mass cytometry and multiplatform genomics define the phenogenomic landscape of breast cancer.
Nature cancer · 2020
|
1 | 1 | 548 | 479,844 |
| HCC_39455893 |
Immunotherapy response induces divergent tertiary lymphoid structure morphologies in hepatocellular carcinoma.
Nature Immunology · 2024
|
1 | 1 | 38 | 61,393 |
| CervicalCancer_CmTSA_41807362 |
Integrative spatial profiling pipeline for determining TME architectures in archival clinical specimens using CmTSA superplex technology.
Cell discovery · 2026
|
1 | 1 | 2 | 1,564,537 |
| HNSCC_41616773 |
Lymph node colonization induces tissue remodeling via immunosuppressive fibroblast-myeloid cell niches supporting metastatic tolerance
Cancer Cell · 2026
|
1 | 1 | 137 | 1,156,046 |
|
HNSCC_41616773 PCF discovery cohort
HNSCCDiscovery_41616773
|
Lymph node colonization induces tissue remodeling via immunosuppressive fibroblast-myeloid cell niches supporting metastatic tolerance
Cancer Cell · 2026
|
1 | 1 | 390 | 1,556,569 |
|
HNSCC_41616773 PCF healthy lymph node cohort
HNSCCHealthyLN_41616773
|
Lymph node colonization induces tissue remodeling via immunosuppressive fibroblast-myeloid cell niches supporting metastatic tolerance
Cancer Cell · 2026
|
1 | 1 | 51 | 1,238,209 |
|
HNSCC_41616773 PCF validation cohort
HNSCCValidation_41616773
|
Lymph node colonization induces tissue remodeling via immunosuppressive fibroblast-myeloid cell niches supporting metastatic tolerance
Cancer Cell · 2026
|
1 | 1 | 34 | 745,842 |
| LUAD_36725934 |
Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma
Cancer Cell · 2023
|
1 | 1 | 416 | 1,635,722 |
| HGSC_39179931 |
Mapping spatial organization and genetic cell-state regulators to target immune evasion in ovarian cancer.
Nature Immunology · 2024
|
3 | 3 | 202 | 2,598,277 |
| BoneMarrow_38714197 |
Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging.
Cell · 2024
|
1 | 1 | 32 | 1,214,574 |
| Neocortex_39779846 |
MERFISH spatial profiling of developing human neocortex.
Nature · 2025
|
1 | 1 | 6 | 404,030 |
| DLBCL_41120574 |
Multi-modal spatial characterization of tumor immune microenvironments identifies targetable inflammatory niches in diffuse large B cell lymphoma.
Nature Genetics · 2025
|
1 | 0 | 6 | 3,512,019 |
| B-NHL_38379051 |
Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities.
Nature cell biology · 2024
|
1 | 1 | 35 | 5,690,284 |
| HCC_39965889 |
Multiomics analysis of immune correlatives in hepatocellular carcinoma patients treated with tremelimumab plus durvalumab.
Gut · 2025
|
1 | 1 | 31 | 387,155 |
| IgAN_38898271 |
Multiscale topology classifies cells in subcellular spatial transcriptomics.
Nature · 2024
|
1 | 0 | 1 | 30,802 |
| Melanoma_40457060 |
PD-1 receptor deficiency enhances CD30(+) T(reg) cell function in melanoma.
Nature Immunology · 2025
|
1 | 0 | 2 | 18,462 |
| GBM_40972572 |
Restraint of cancer cell plasticity by spatial homotypic clustering.
Cancer Cell · 2025
|
1 | 0 | 4 | 239,436 |
| DLBCL_41874448 |
Same-slide spatial multi-omics integration with IN-DEPTH reveals tumor virus-linked spatial reorganization of the tumor microenvironment
Cancer Discovery · 2025
|
2 | 2 | 86 | 1,355,312 |
| Melanoma_40148341 |
SIMVI disentangles intrinsic and spatial-induced cellular states in spatial omics data.
Nature Communications · 2025
|
1 | 1 | 25 | 56,761 |
|
UlcerativeColitis_38374043 CosMx 960-plex Run 1
UlcerativeColitisRun1_38374043
|
Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.
Nature Communications · 2024
|
1 | 1 | 17 | 66,379 |
|
UlcerativeColitis_38374043 CosMx 1000-plex Run 2 Longitudinal
UlcerativeColitisRun2_38374043
|
Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis.
Nature Communications · 2024
|
1 | 1 | 73 | 126,368 |
| TNBC_38194915 |
Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer.
Cancer Cell · 2024
|
1 | 1 | 27 | 2,597,738 |
| NSCLC_40408481 |
Single-cell multimodal analysis reveals tumor microenvironment predictive of treatment response in non-small cell lung cancer.
Science advances · 2025
|
1 | 1 | 257 | 1,450,507 |
| BrainTumor_36725935 |
Single-cell spatial immune landscapes of primary and metastatic brain tumours.
Nature · 2023
|
1 | 1 | 393 | 1,163,362 |
| NormalSkin_41872488 |
Single-cell spatial transcriptomic analysis of human skin anatomy.
Nature Genetics · 2026
|
1 | 1 | 114 | 1,201,886 |
| HCC_39304772 |
Spatial analysis reveals targetable macrophage-mediated mechanisms of immune evasion in hepatocellular carcinoma minimal residual disease.
Nature cancer · 2024
|
1 | 1 | 124 | 1,065,284 |
| SCN_41720090 |
Spatial and single-cell transcriptomic atlas of human suprachiasmatic nucleus
Neuron · 2025
|
2 | 2 | 2 | 23,076 |
| CastlemanDisease_40593805 |
Spatial and single cell mapping of castleman disease reveals key stromal cell types and cytokine pathways.
Nature Communications · 2025
|
1 | 1 | 18 | 1,299,746 |
| ASD_42288509 |
Spatial architecture of autism pathogenesis reveals mosaic structural disarray during early development.
Nature Communications · 2026
|
1 | 0 | 71 | 1,515,114 |
| DKD_42056516 |
Spatial atlas of diabetic kidney disease reveals a B cell-rich subgroup.
Nature · 2026
|
2 | 2 | 64 | 4,337,862 |
| Melanoma_35363543 |
Spatially mapping the immune landscape of melanoma using imaging mass cytometry.
Science Immunology · 2022
|
1 | 1 | 72 | 272,135 |
| PDAC_39227743 |
Spatially resolved analysis of pancreatic cancer identifies therapy-associated remodeling of the tumor microenvironment.
Nature Genetics · 2024
|
1 | 1 | 16 | 717,493 |
| PDAC_40269162 |
Spatial mapping of transcriptomic plasticity in metastatic pancreatic cancer.
Nature · 2025
|
1 | 1 | 90 | 82,348 |
| Neuroblastoma_41918107 |
Spatial multi-omics characterization of neuroblastoma reveals ferroptosis-associated metabolic features in high-risk tumors.
Genome medicine · 2026
|
1 | 1 | 24 | 832,243 |
| OSCC_41707652 |
Spatial single-cell analysis reveals tumor microenvironment signatures predictive of oral cavity cancer outcome
Cell Reports Medicine · 2026
|
1 | 1 | 92 | 708,261 |
| HCC_39327501 |
Spatial single-cell protein landscape reveals vimentin(high) macrophages as immune-suppressive in the microenvironment of hepatocellular carcinoma.
Nature cancer · 2024
|
1 | 1 | 288 | 3,231,437 |
| IBD_42049732 |
Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials.
Nature Communications · 2026
|
1 | 1 | 34 | 43,034 |
| PulmonaryFibrosis_39901013 |
Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis.
Nature Genetics · 2025
|
1 | 1 | 45 | 790,934 |
| HGSOC_38570491 |
Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones
Nature Communications · 2024
|
1 | 0 | 1 | 39,959 |
| RheumatoidArthritis_39609125 |
Synovial tissue myeloid dendritic cell subsets exhibit distinct tissue-niche localization and function in health and rheumatoid arthritis.
Immunity · 2024
|
1 | 0 | 60 | 110,567 |
| SPATCH_41107232 |
Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms across human tumors
Nature Communications · 2025
|
4 | 4 | 18 | 4,948,582 |
| BRCA_31959985 |
The single-cell pathology landscape of breast cancer.
Nature · 2020
|
1 | 1 | 381 | 855,668 |
| CRC_40189697 |
The single-cell spatial landscape of stage III colorectal cancers.
NPJ precision oncology · 2025
|
1 | 1 | 170 | 903,125 |
| Intestine_39843748 |
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted.
Nature · 2025
|
2 | 2 | 18 | 3,284,840 |
| BRCA_35063072 |
Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma.
Cell · 2022
|
1 | 1 | 79 | 69,672 |
|
LiverCancer_41723121 HCC cohort
HCC_41723121
|
Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer
Nature Communications · 2026
|
1 | 1 | 9 | 1,446,124 |
|
LiverCancer_41723121 iCCA cohort
ICC_41723121
|
Tumor cell villages define the co-dependency of tumor and microenvironment in liver cancer
Nature Communications · 2026
|
1 | 1 | 6 | 901,465 |
|
MERFISH 500-plex Vizgen showcase
MERFISH_500_Vizgen
|
Vizgen MERFISH 500-plex official data release
Vizgen
|
1 | 1 | 18 | 10,196,835 |
|
MERFISH 815-plex Vizgen showcase
MERFISH_815_Vizgen
|
Vizgen MERFISH 815-plex official data release
Vizgen
|
1 | 1 | 6 | 1,051,006 |
|
MERFISH 960-plex Vizgen showcase
MERFISH_960_Vizgen
|
Vizgen MERFISH 960-plex official data release
Vizgen
|
1 | 1 | 3 | 394,181 |