Chenlei Hu, Mehdi Borji, Giovanni J. Marrero, Vipin Kumar, Jackson A. Weir, Sachin V. Kammula, Evan Z. Macosko, Fei Chen
{"title":"Scalable spatial transcriptomics through computational array reconstruction","authors":"Chenlei Hu, Mehdi Borji, Giovanni J. Marrero, Vipin Kumar, Jackson A. Weir, Sachin V. Kammula, Evan Z. Macosko, Fei Chen","doi":"10.1038/s41587-025-02612-0","DOIUrl":null,"url":null,"abstract":"<p>Spatial transcriptomics enables gene expression mapping within tissues but is often limited by imaging constraints. We present an imaging-free approach that reconstructs spatial barcode locations using molecular diffusion and dimensionality reduction. Validated against ground truth imaging, our method achieves high fidelity and scales to centimeter-sized tissues. This approach enhances spatial transcriptomics’ accessibility and throughput, enabling large-scale studies without specialized imaging equipment.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"20 1","pages":""},"PeriodicalIF":41.7000,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Nature biotechnology","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1038/s41587-025-02612-0","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Spatial transcriptomics enables gene expression mapping within tissues but is often limited by imaging constraints. We present an imaging-free approach that reconstructs spatial barcode locations using molecular diffusion and dimensionality reduction. Validated against ground truth imaging, our method achieves high fidelity and scales to centimeter-sized tissues. This approach enhances spatial transcriptomics’ accessibility and throughput, enabling large-scale studies without specialized imaging equipment.
期刊介绍：
Nature Biotechnology is a monthly journal that focuses on the science and business of biotechnology. It covers a wide range of topics including technology/methodology advancements in the biological, biomedical, agricultural, and environmental sciences. The journal also explores the commercial, political, ethical, legal, and societal aspects of this research.
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In summary, Nature Biotechnology is a comprehensive journal that covers both the scientific and business aspects of biotechnology. It strives to provide researchers with valuable research papers and news while also delivering important scientific advancements to the business community.
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