ArticleNature communications2023
Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers, 1 of them a synthesis that pooled it.
What it found
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Who cites it
84 citing papers in PubMed, 1 synthesis or guideline pooled it, 103 citations in OpenAlex.
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- STAT3D as a new image-tailored Xenium-based spatial transcriptomics tool for accurately dissecting the tumor microenvironment.Nucleic acids research · 2026Article
- Conserved Metastatic Cell States and Spatial Immune Microenvironment Remodeling Define Pancreatic Cancer Liver Metastases.bioRxiv : the preprint server for biology · 2026Article
- Distinct Spatial Immune Architectures in Tumor and Tumor-Adjacent Tissues of Early-Stage Non-Small Cell Lung Cancer.bioRxiv : the preprint server for biology · 2026Article
- Analysis of multicellular anatomical structures from spatial omics data using sosta.PLoS computational biology · 2026Article
- Iterative multiplex imaging cytometry for cross-species analyses of in situ tissue leukocytes.Journal of immunological methods · 2026Article
- The cortical microenvironment drives early immune organization and controls early osteoclastogenesis in bone healing.Nature communications · 2026Article
- MuSpAn: a toolbox for multiscale spatial analysis.Nature communications · 2026Article
- SpatialFlux: an R package for distance gradient analysis in spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Single-nucleus multimodal spatial transcriptomics reveals spatial colocalization of neoantigen-expressing tumor cells and cognate T cells.Nature biotechnology · 2026Article
- Stromal Cell Subsets Modulate T-cell Infiltration in Early Breast Cancer.Cancer research communications · 2026Article
- Cancer Heterogeneity and Cancer Cell Plasticity: Molecular Mechanisms and Precision Therapy.MedComm · 2026Review
- Differences in T-cell Densities and Neighborhood Patterns in Human Colorectal Adenomas and Sessile Serrated Lesions.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2026Article
- Spatial transcriptomics identifies immune-stromal niches associated with cancer in adult dermatomyositis.Nature communications · 2026Article
- Melanoma cell states shape spatial tumor-immune ecosystems to dictate the efficacy of anti-PD1 immunotherapy.Journal for immunotherapy of cancer · 2026Article
- Tumor-resident T cells and dendritic cells form an in situ archetype during immunotherapy response in melanoma.Nature communications · 2026Article
- Estimating tumour immune infiltration: methodological convergence across histology and spatial technologies.Briefings in bioinformatics · 2026Review
- Global data-water symbiosis reduces AI infrastructure's carbon and water footprint.Environmental science and ecotechnology · 2026Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
20 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Spatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and clinical features, but there is significant lag in the development of downstream analysis methods and benchmarking tools. Here we present SPIAT (spatial image analysis of tissues), a spatial-platform agnostic toolkit with a suite of spatial analysis algorithms, and spaSim (spatial simulator), a simulator of tissue spatial data. SPIAT includes multiple colocalization, neighborhood and spatial heterogeneity metrics to characterize the spatial patterns of cells. Ten spatial metrics of SPIAT are benchmarked using simulated data generated with spaSim. We show how SPIAT can uncover cancer immune subtypes correlated with prognosis in cancer and characterize cell dysfunction in diabetes. Our results suggest SPIAT and spaSim as useful tools for quantifying spatial patterns, identifying and validating correlates of clinical outcomes and supporting method development.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.