ArticleNature biotechnology2026
Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.
Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
25 citing papers in PubMed.
- Unveiling the role of spatial transcriptomics in the analysis of the tumor immune microenvironment (Review).International journal of molecular medicine · 2026Review
- Granaticin biosynthesis and engineering: mechanistic understanding, production bottlenecks, and computational opportunities.World journal of microbiology & biotechnology · 2026Review
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
- Review
- Single-cell multiomics identifies an ALDH9A1-carnitine signaling axis driving resistance of NSCLC to immunotherapy.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Spatial ecotype in tumor immune exclusion: from spatial architecture to therapeutic strategies.Molecular cancer · 2026Review
- Transforming subcellular spatial transcriptomics: deep learning models for cell segmentation.Nucleic acids research · 2026Review
- Genetic influences on haematopoiesis.Nature reviews. Genetics · 2026Review
- Spatial transcriptomic profiling of ovarian clear cell carcinoma reveals heterogeneity in OXPHOS and EMT gradients.Nature communications · 2026Article
- Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.Nature biotechnology · 2026Article
- Spatial Heterogeneity of Intratumoral Microbiota and Its Roles in Tumor-Microbiota Interactions and Therapeutic Implications.Pathogens (Basel, Switzerland) · 2026Review
- Fascia as a Functional System in Health and Disease: From Fundamental Biology to Assessment and Targeted Interventions.International journal of molecular sciences · 2026Review
- Tumor microenvironment-specific nanomedicine: from biology-driven to multi-omics-guided precision engineering.Journal of hematology & oncology · 2026Review
- CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments.PLoS computational biology · 2026Article
- Review
- Antibiotic-resistant infections cured by calcium deposition.Nature biotechnology · 2026Article
- Reconstructing biologically coherent cellular profiles from imaging-based spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- DNA-drug conjugates enable logic-gated drug delivery amplified by hybridization chain reactions.Nature biotechnology · 2026Article
- The good, the bad, and the ugly: opportunities, challenges, and pitfalls in spatial proteomics modeling.Briefings in bioinformatics · 2026Review
- Convergence of machine learning and genomics for precision oncology.Nature reviews. Cancer · 2026Review
Corrections and comments
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Authors and funding
28 authors.
Funding
Abstract
Spatial transcriptomics lacks standardized metrics for evaluating imaging-based in situ hybridization technologies across sites. In this study, we generated the Spatial Touchstone (ST) dataset from six tissue types across several global sites with centralized sectioning, analyzed on both Xenium and CosMx platforms. These platforms were selected for their widespread use and distinct chemistries. We assessed reproducibility, sensitivity, dynamic ranges, signal-to-noise ratio, false discovery rates, cell type annotation and congruence with single-cell profiling. This study offers ST standardized operating procedures (STSOPs) and an open-source software, SpatialQM, enabling evaluation of samples across all technical metrics and direct imputation of cell annotations. The generated imaging-based spatial transcriptomics data repository comprises 254 spatial profiles, incorporating both public and newly generated ST datasets in a web-based application, which enables analysis and comparison of user data against an extensive collection of imaging-based datasets. Finally, we establish best practices and metrics to evaluate and integrate imaging-based multi-omics data from single cells into spatial transcriptomics to spatial proteomics.
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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.