ArticleNature biotechnology2025
High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes.
Article in Nature biotechnology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
10 citing papers in PubMed.
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology.Nature methods · 2026Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- Review
- ModelistsGCN: a multimodal graph convolutional network framework for single-cell spatial transcriptomic cell typing.Briefings in bioinformatics · 2026Article
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Base editors model mitochondrial disease.Nature biotechnology · 2026Article
- Efficient mitochondrial A-to-G base editors for the generation of mitochondrial disease models.Nature biotechnology · 2026Article
- Design of a Multi-epitope Antigen for Toxoplasmosis Diagnosis: An Immunoinformatics Approach.Acta parasitologica · 2025Article
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
Spatial RNA imaging has not been widely adopted because conventional fluorescence microscopy is limited to only a few channels and the cyclic reactions needed to increase multiplexing in techniques such as sequential fluorescence in situ hybridization require sophisticated instrumentation. Here, we introduce 'profiling of RNA in situ through single-round imaging' (PRISM), a method that expands coding capacity through color intensity grading. Using a radius vector filtering strategy to ensure the distinguishability of codewords in color space, PRISM achieves up to 64-plex color-barcoded RNA imaging in a single imaging round with conventional microscopes. We validate PRISM's versatility across various tissues by generating a three-dimensional (3D) atlas of mouse embryonic development from E12.5 to E14.5, a quasi-3D tumor-normal transition landscape of human hepatocellular carcinoma and a 3D cell atlas and subcellular RNA localization landscapes of mouse brain. Additionally, we show the critical role of cancer-associated fibroblasts in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments.
Identifiers
41168495What OpenQuestion holds
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.